Changing the Landscape: A New Strategy for Estimating Large Phylogenies

Quicke, Donald L. J.; Taylor, Joshua F.; Purvis, Andy

doi:10.1080/10635150119012

Cited by 36 publications

(34 citation statements)

References 17 publications

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“…We estimated phylogenies using maximum parsimony (MP) in PAUP Ã version 4.0b10 (Swofford 2002). We treated gaps as missing data and, following Quicke et al (2001), conducted an initial heuristic search with 10 000 random additions and TBR branch swapping, holding one tree per replicate. We then used the trees generated by the initial search as starting trees for a second heuristic search, in which we saved multiple trees.…”

Section: (B) Molecular Methodsmentioning

confidence: 99%

Convergent incidences ofWolbachiainfection in fig wasp communities from two continents

Haine

Cook

2005

Proc. R. Soc. B.

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Wide surveys suggest that Wolbachia bacteria infect ca. 20% of all insect species, but particular taxonomic or ecological groups may display significantly higher or lower incidences. We studied 61 fig wasp species in Australia and found the highest known incidence (67%) of infection in a targeted study of this nature. A comparable study in Panama reported a similar figure (59%), confirming the exceptionally high incidence of Wolbachia in fig wasps. Importantly, these are two independent estimates of Wolbachia incidence in fig wasp communities, because no host species, or even genera, are shared between localities. The high level of infection may reflect enhanced opportunities for horizontal transmission inside fig fruits. Although incidence was similar in Panama and Australia, the actual strains involved were different and region-specific. Local strains were shared by several host species, although there was often no obvious (direct) ecological link between two hosts with the same infection.

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Section: (B) Molecular Methodsmentioning

confidence: 99%

Convergent incidences ofWolbachiainfection in fig wasp communities from two continents

Haine

Cook

2005

Proc. R. Soc. B.

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“…Searches were carried out to the limit allowed by computer memory. No shorter trees were recovered by using the iterative reweighting strategy proposed by Quicke et al (2001). The largest numbers of trees from analyses I and II are identical (341 200), and correspond to the maximum number of trees that could be stored at the end of the tree search.…”

Section: Data Matrix Processingmentioning

confidence: 99%

A supertree of early tetrapods

Ruta

Jeffery

Coates

2003

Proc. R. Soc. Lond. B

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A genus-level supertree for early tetrapods is built using a matrix representation of 50 source trees. The analysis of all combined trees delivers a long-stemmed topology in which most taxonomic groups are assigned to the tetrapod stem. A second analysis, which excludes source trees superseded by more comprehensive studies, supports a deep phylogenetic split between lissamphibian and amniote total groups. Instances of spurious groups are rare in both analyses. The results of the pruned second analysis are mostly comparable with those of a recent, character-based and large-scale phylogeny of Palaeozoic tetrapods. Outstanding areas of disagreement include the branching sequence of lepospondyls and the content of the amniote crown group, in particular the placement of diadectomorphs as stem diapsids. Supertrees are unsurpassed in their ability to summarize relationship patterns from multiple independent topologies. Therefore, they might be used as a simple test of the degree of corroboration of nodes in the contributory analyses. However, we urge caution in using them as a replacement for character-based cladograms and for inferring macroevolutionary patterns.

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“…This strategy (see Quicke et al 2000) allows searching in a wide area of tree space and maximises chances of finding multiple islands of equally parsimonious trees (Maddison 1991;Goloboff 1999). Thereafter, all trees from the different islands were used as starting trees for further TBR searches with maxtrees effectively unlimited.…”

Section: Separate Male and Female Analyses (Analyses 1 And 2)mentioning

confidence: 99%

Phylogeny within the Chondracanthidae (Poecilostomatoida, Copepoda)

Østergaard¹,

Boxshall²,

Quicke³

2003

Zoologica Scripta

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AbstractØstergaard, P., Boxshall, G. A. & Quicke, D. L. J. (2002). Phylogeny within the Chondracanthidae (Poecilostomatoida, Copepoda). -Zoologica Scripta, 00, 000-000.The existing systematics of the Chondracanthidae is based predominantly on female characters and divides them into two subfamilies; Chondracanthinae and Lernentominae. Phylogenetic analyses using maximum parsimony were performed using 186 male and female characters. Different trees were generated when male and female characters were analysed separately. Differential weighting showed that the female characters were dominant but not to a great extent and subsequent analyses were run with both partitions combined. Different trees were generated depending on the character setting (unordered, ordered and irreversible-up). Interestingly, a basal backbone comprising the same nine ingroup taxa was present in all the trees, although the sequence of those taxa could differ. Constraining the two subfamilies to be monophyletic caused tree length to be increased and the Templeton and Kishino-

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Changing the Landscape: A New Strategy for Estimating Large Phylogenies

Cited by 36 publications

References 17 publications

Convergent incidences ofWolbachiainfection in fig wasp communities from two continents

Convergent incidences ofWolbachiainfection in fig wasp communities from two continents

A supertree of early tetrapods

Phylogeny within the Chondracanthidae (Poecilostomatoida, Copepoda)

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