The Discovery and Importance of Multiple Islands of Most-Parsimonious Trees

Maddison, David R.

doi:10.1093/sysbio/40.3.315

Cited by 723 publications

(377 citation statements)

References 23 publications

Supporting

Mentioning

366

Contrasting

Unclassified

Order By: Relevance

“…Anseriformes lie Major avian clades plotted in a wing phylomorphospace described by principal components (PC) 1 and 2 for the 105 taxon sample. The phylogenetic tree [51] is mapped in this morphospace, with internal nodes placed according to a squared-change parsimony optimization [55]. Major changes in wing shape along the two PC axes are depicted on deformation grids from the consensus wing (insets).…”

Section: Resultsmentioning

confidence: 99%

“…MESQUITE (v. 2.75; [86]) was used to map PC 1 and 2 which contained the wing shape information onto the reference phylogeny. Each character was traced onto the tree using the 'reconstruct ancestral state' module of MESQUITE with weighted squaredchange parsimony [55]. See the electronic supplementary material for further information.…”

Section: (C) Phylogenetic Signal and Ancestral State Reconstructionmentioning

confidence: 99%

See 1 more Smart Citation

The evolution of avian wing shape and previously unrecognized trends in covert feathering

Wang

Clarke

2015

Proc. R. Soc. B.

View full text Add to dashboard Cite

ResearchCite this article: Wang X, Clarke JA. 2015 The evolution of avian wing shape and previously unrecognized trends in covert feathering. Proc. R. Soc. Avian wing shape has been related to flight performance, migration, foraging behaviour and display. Historically, linear measurements of the feathered aerofoil and skeletal proportions have been used to describe this shape. While the distribution of covert feathers, layered over the anterior wing, has long been assumed to contribute to aerofoil properties, to our knowledge no previous studies of trends in avian wing shape assessed their variation. Here, these trends are explored using a geometric-morphometric approach with landmarks describing the wing outline as well as the extent of dorsal and ventral covert feathers for 105 avian species. We find that most of the observed variation is explained by phylogeny and ecology but shows only a weak relationship with previously described flight style categories, wing loading and an investigated set of aerodynamic variables. Most of the recovered variation is in greater primary covert feather extent, followed by secondary feather length and the shape of the wing tip. Although often considered a plastic character strongly linked to flight style, the estimated ancestral wing morphology is found to be generally conservative among basal parts of most major avian lineages. The radiation of birds is characterized by successive diversification into largely distinct areas of morphospace. However, aquatic taxa show convergence in feathering despite differences in flight style, and songbirds move into a region of morphospace also occupied by basal taxa but at markedly different body sizes. These results have implications for the proposed inference of flight style in extinct taxa.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: (C) Phylogenetic Signal and Ancestral State Reconstructionmentioning

confidence: 99%

The evolution of avian wing shape and previously unrecognized trends in covert feathering

Wang

Clarke

2015

Proc. R. Soc. B.

View full text Add to dashboard Cite

show abstract

“…Separate analyses were performed for the complete data set (5S gene + spacer) and for subsets of the data (5S only, spacer only). In all cases, at least five independent heuristic searches were conducted per data set using the random data addition option, in an effort to find shorter "islands" of trees than those recovered from initial searches (Maddison 1991). To evaluate relative levels of support for individual clades, strict consensus trees were generated for all topologies found that were up to five steps longer than the most parsimonious trees ("decay analysis" : Bremer 1988;Donoghue et al 1992).…”

Section: S Rdna Copy-number Estimationmentioning

confidence: 99%

Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons

et al. 1996

View full text Add to dashboard Cite

5S RNA genes and their nontranscribed spacers are tandemly repeated in plant genomes at one or more chromosomal loci. To facilitate an understanding of the forces that govern 5S rDNA evolution, copy-number estimation and DNA sequencing were conducted for a phylogenetically well-characterized set of 16 diploid species of cotton (Gossypium) and 4 species representing allopolyploid derivatives of the diploids. Copy number varies over twentyfold in the genus, from approximately 1,000 to 20,000 copies/2C genome. When superimposed on the organismal phylogeny, these data reveal examples of both array expansion and contraction. Across species, a mean of 12% of nucleotide positions are polymorphic within individual arrays, for both gene and spacer sequences. This shows, in conjunction with phylogenetic evidence for ancestral polymorphisms that survive speciation events, that intralocus concerted evolutionary forces are relatively weak and that the rate of interrepeat homogenization is approximately equal to the rate of speciation. Evidence presented also shows that duplicated 5S rDNA arrays in allopolyploids have retained their subgenomic identity since polyploid formation, thereby indicating that interlocus concerted evolution has not been an important factor in the evolution of these arrays. A descriptive model, one which incorporates the opposing forces of mutation and homogenization within a selective framework, is outlined to account for the empirical data presented. Weak homogenizing forces allow equivalent levels of sequence polymorphism to accumulate in the 5S gene and spacer sequences, but fixation of mutations is nearly prohibited in the 5S gene. As a consequence, fixed interspecific differences are statistically underrepresented for 5S genes. This result explains the apparent paradox that despite similar levels of gene and spacer diversity, phylogenetic analysis of spacer sequences yields highly resolved trees, whereas analyses based on 5S gene sequences do not.

show abstract

“…These operations were first introduced by Robinson [4] as a measure of the similarity between two unrooted trees having the same set of leaf labels. Since then, this notion has been extended in a number of ways for both rooted and unrooted trees [1][2][3]. Our focus in this paper is solely on the tree bisection and reconnection (TBR) operation.…”

Section: Introductionmentioning

confidence: 99%

“…Perhaps more importantly for our purposes, the TBR operation induces a metric on the space of unrooted trees, and is used as the basis for heuristic algorithms that search this space for the best tree under some optimization constraints [2,3].…”

Section: Introductionmentioning

confidence: 99%

Bounds on the Size of the TBR Unit-Neighbourhood

Humphries

2010

Ann. Comb.

View full text Add to dashboard Cite

In this paper, we study the unit-neighbourhood of the tree bisection and reconnection operation on unrooted binary phylogenetic trees. Specifically, we provide a recursive method to calculate the size of the unit-neighbourhood for any tree in the space T n of unrooted binary phylogenetic trees with n-leaves. We also give both upper and lower bounds on this size for all trees in T n , and characterize those trees for which the stated upper bound is sharp.

show abstract

The Discovery and Importance of Multiple Islands of Most-Parsimonious Trees

Cited by 723 publications

References 23 publications

The evolution of avian wing shape and previously unrecognized trends in covert feathering

The evolution of avian wing shape and previously unrecognized trends in covert feathering

Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons

Bounds on the Size of the TBR Unit-Neighbourhood

Contact Info

Product

Resources

About