Gene trees

Oota, S. and Saitou, N. (1999). Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol. Biol. Evol. 16, 856-867. 

Fig. 10.4. Maximum likelihood phylogenetic trees of (a) pyruvate ferredoxin oxidoreductase (PFO) and (b) Fe-hydrogenase genes. Trees and branch support were obtained as in Fig. 10.3. Branch support above branches is shown only for those nodes with greater than 85% bootstrap support. Anaerobic eukaryotes are shown in bold...

A problem always faced in designing an evolutionary investigation is judging how many individuals need to be analyzed from a particular species or population. This problem manifests itself across the range of questions, from inferring species trees from gene trees to comparing variation within and between populations. 

Doyle, J. (1992) Gene trees and species trees molecular systematics as one-character taxonomy. Syst. Bot., 17,144-63. 

When the sequence polymorphisms in ACE are resolved into haplotypes and a gene tree constructed [52], the pattern of variation in ACE reveals the presence of two major dades that are detected by the Alu indel (Figure 3.3). Because the deletion dade has been consistently associated with cardiovascular disease pathology including myocardial infarction, arterial hyper-... 

A consensus parsimony gene tree for ACE haplotypes. The relative frequency of each haplotype is indicated by the area of the circle. 

Figure 2 tub2 gene tree of Epichloe spp. form different hosts based on maximum parsimony analysis. The bar represents 5 inferred nucleotide substitutions. Numbers at branches are the percentages of trees containing the corresponding clade based on 500 bootstrap replications. Values greater than 70% are considered supportive of the clade. (Modified from Schardl and Leuchtmann, 1999.)... 

Simulation smdies indicate that UPGMA performs poorly over a broad range of tree shape space (Huelsenbeck, 1995). The use of this method is not recommended it is mentioned here only because its application seems to persist, as evidenced by UPGMA gene trees appearing in publications (Huelsenbeck, 1995). 

Saitou, N. (1996). Reconstruction of gene trees from sequence data. Methods Enzymol. 266, 427-449. 

Avise, J.C., Ankney, C.D., Nelson, W.S. (1990). Mitochondrial gene trees and the evolutionary relationship of Mallard and Black ducks. Evolution, 44, 1109-19. 

Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Mol Biol Evol 5 568-583 Polhili RM (1981) Papilionoideae. In Polhill RM, Raven PH (eds) Advances in Legume Systematics, Part 1. Royal Botanic Gardens, Kew, pp 191-208... 

Figure 1. Illustration of "gene trees" versus "species trees". The lines represent alleles within lineages while the inclusive shaded areas represent the species or populations. In case A the species tree and gene tree coincide both in terms of topology and times of divergence. In case B they coincide with respect to topology but not in time of divergence.

In case C, the gene tree and species tree have different topologies. Modified from Pamillo and Nei (1988). 

Pamilo P, Nel M (1988) Relationship between gene trees and species trees. Mol Biol Evol 5 568-583... 

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