Search results
Aug 1, 2015 · Reconstruction of phylogenetic relationships can be an arduous and prolonged task. Large numbers of specimens must be examined to produce even larger numbers of potentially informative traits. These descriptive data are scored and fed into phylogenetic analysis routines to determine which of the myriad possible phylogenies are supported by the ...
- Donald L. Swiderski
- 2001
Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used differences and similarities between species as a major source of evidence in The Origin of Species.
- Why Phylogeny Matters
- No Subclasses
- Phylogeny Reconstruction. A Primer
- Molecular Clocks. Rates and Dates of Gene Diversification
- Summary and Future Prospects
- Acknowledgments
Many biologists agree that a phylogenetic tree of relationships should be the central underpinning of research in many areas of biology. Comparisons of plant species or gene sequences in a phylogenetic context can provide the most meaningful insights into biology. This important realization is now apparent to researchers in diverse fields, includin...
Perhaps the best known classification of angiosperms is that of Cronquist (1981), who recognized six subclasses of dicots, Magnoliidae, Hamamelidae, Rosidae, Dilleniidae, Caryophyllidae, and Asteridae, and five subclasses of monocots, although these were followed less frequently. Molecular phylogenies indicate that these subclasses, like the classe...
Alignment
Alignment of nucleotide and amino acid sequences is a major consideration, particularly in studies of genes from divergent taxa (e.g. rice and Arabidopsis). It seems obvious to state that the phylogenetic analysis of sequences begins with the appropriate alignment of the data themselves, yet alignment remains one of the most difficult and poorly understood facets of molecular data analysis. Detailed coverage of the topic is beyond the scope of this Update, but excellent overviews are provided...
Life after Neighbor Joining
Inferences of orthology require phylogenetic analysis. Although expression patterns and knowledge of function may provide clues to orthology relationships, orthology, by definition, requires historical analysis to disentangle the products of gene duplication and speciation (for useful review of orthology and paralogy, see Doyle and Gaut, 2000; Jensen, 2001; Koonin, 2001). Thus, molecular biologists and geneticists suddenly need to become phylogeneticists. Although molecular phylogeny reconstr...
Internal Support for Clades
Some measure of internal support for clades should be provided on all phylogenetic trees. Resampling approaches, such as the bootstrap and the jackknife, are easily computed using PAUP* for parsimony, NJ, and ML analyses, and parsimony jackknifing is performed by Jac (Farris et al., 1996). The pros and cons of the jackknife versus bootstrap have been discussed (e.g. Farris et al., 1996; Soltis and Soltis, 2003). A reasonable number of replications should be employed, but “reasonable” varies w...
Many efforts to date evolutionary divergences using a molecular clock have yielded age estimates that are grossly inconsistent with the fossil record, regardless of method of tree construction. For example, molecular-based estimates of divergence times in plants reveal a vast range of dates. Using molecular data, the age of the angiosperms has been...
An exciting recent development is the merging of phylogenetics and genomics. Phylogenetic hypotheses have become the framework for the choice of organisms in genomic analyses, and more and more molecular biologists are using phylogenetic trees to guide their sampling of taxa for comparative research. This trend will continue. Systematics is moving ...
We thank Jeff Doyle, Bernie Hauser, Alice Harmon, and two anonymous reviewers for helpful comments on earlier drafts of this paper.
- Douglas E. Soltis, Pamela S. Soltis
- 2003
Jan 25, 2010 · Using A to represent the phylogenetic relatedness matrix, we show that several recent comparative papers are variations of a common theme – phylogenetic meta-analysis. However, our main point is that this model is also a relatively minor variation of the basic mixed model, for which software has been available for some time.
- Jarrod Hadfield, S. Nakagawa
- 2010
Phylogenetic comparative methods are important tools in biology, providing insights into the way traits evolve. There are many technical resources describing how these methods work. Our aim here is to complement these with an overview of the types of biological questions that can be addressed by different methods and to outline potential pitfalls and considerations when embarking on ...
Sep 1, 2002 · In The Comparative Method in Evolutionary Biology, Harvey and Pagel (1991) state, “An assessment of phylogenetic relationships is a prerequisite for a successful comparative analysis” (p. 35). The truthfulness of this pronouncement depends upon the inferences one is trying to make with that comparative analysis; however, for those who are not familiar with the general principles and ...
People also ask
What are phylogenetic comparative methods?
Are phylogenetic analyses a virtue of Comparative Biology?
Is phylogenetic analysis a prerequisite for a successful comparative analysis?
Which phylogeny method is most useful for Comparative Biology?
Why are phylogenetic comparisons important?
Can we compare phylogenetic relationships between organisms?
Feb 11, 2009 · Each mega-phylogeny matrix assembly analysis presented here was run on a Linux laptop with 1 GB RAM and a 2.4 Ghz dual-core processor. The phylogenetic analyses were conducted on an eight-way SMP Linux computer with 2.4 Ghz processors and 32 GB of RAM using RAxML (vers. 7.0.4; ). The steps that are novel for matrix assembly are described ...
