Multiple Gene Trees Research Articles

Stochastic Models for Horizontal Gene Transfer

Horizontal gene transfer (HGT) plays a critical role in evolution across all domains of life with important biological and medical implications. I propose a simple class of stochastic models to examine HGT using multiple orthologous gene alignments. The models function in a hierarchical phylogenetic framework. The top level of the hierarchy is based on a random walk process in "tree space" that allows for the development of a joint probabilistic distribution over multiple gene trees and an unknown, but estimable species tree. I consider two general forms of random walks. The first form is derived from the subtree prune and regraft (SPR) operator that mirrors the observed effects that HGT has on inferred trees. The second form is based on walks over complete graphs and offers numerically tractable solutions for an increasing number of taxa. The bottom level of the hierarchy utilizes standard phylogenetic models to reconstruct gene trees given multiple gene alignments conditional on the random walk process. I develop a well-mixing Markov chain Monte Carlo algorithm to fit the models in a Bayesian framework. I demonstrate the flexibility of these stochastic models to test competing ideas about HGT by examining the complexity hypothesis. Using 144 orthologous gene alignments from six prokaryotes previously collected and analyzed, Bayesian model selection finds support for (1) the SPR model over the alternative form, (2) the 16S rRNA reconstruction as the most likely species tree, and (3) increased HGT of operational genes compared to informational genes.

Inferring confidence sets of possibly misspecified gene trees.

The problem of inferring confidence sets of gene trees is discussed without assuming that the substitution model or the branching pattern of any of the investigated trees is correct. In this case, widely used methods to compare genealogies can give highly contradicting results. Here, three methods to infer confidence sets that are robust against model misspecification are compared, including a new approach based on estimating the confidence in a specific tree using expected-likelihood weights. The power of the investigated methods is studied by analysing HIV-1 and mtDNA sequence data as well as simulated sequences. Finally, guidelines for choosing an appropriate method to compare multiple gene trees are provided.

Utility of Low-Copy Nuclear Gene Sequences in Plant Phylogenetics

Low-copy nuclear genes in plants are a rich source of phylogenetic information. They hold a great potential to improve the robustness of phylogenetic reconstruction at all taxonomic levels, especially where universal markers such as cpDNA and nrDNA are unable to generate strong phylogenetic hypotheses. Low-copy nuclear genes, however, remain underused in plant phylogenetic studies due to practical and theoretical complications in unraveling the evolutionary dynamics of nuclear gene families. The lack of the universal markers or universal PCR primers of low-copy nuclear genes has also hampered their phylogenetic utility. It has recently become clear that low-copy nuclear genes are particularly helpful in resolving close interspecific relationships and in reconstructing allopolyploidization in plants. Gene markers that are widely, if not universally, useful have begun to emerge. Although utilizing low-copy nuclear genes usually requires extra lab work such as designing PCR primers, PCR-cloning, and/or Southern blotting, rapid accumulation of gene sequences in the databases and advances in cloning techniques have continued to make such studies more feasible. With the growing number of theoretical studies devoted to the gene tree and species tree problem, a solid foundation for reconstructing complex plant phylogenies based on multiple gene trees began to build. It is also realized increasingly that fast evolving introns of the low-copy nuclear genes will provide much needed phylogenetic information around the species boundary and allow us to address fundamental questions concerning processes of plant speciation. Phylogenetic and molecular evolutionary analyses of developmentally important genes will add a new dimension to systematic and evolutionary studies of plant diversity.

A data based parsimony method of cophylogenetic analysis

Phylogenies of closely interacting groups, such as hosts and parasites, are seldom completely congruent. Incongruence can arise from biologically meaningful differences in the histories of the two groups, or can be generated by artifactual differences that are merely the result of incorrect phylogenies with weakly supported nodes. We present a method that distinguishes between these sources of incongruence and identifies lineages that are responsible for significant differences between phylogenies. We use the logic of conditional combination in that we first test for statistically significant incongruence using the partition homogeneity test. Then we remove all possible combinations of taxa until a non‐significant result of this test is achieved. Finally, we construct a ‘combined evidence’ phylogeny and then reposition the incongruent taxa. This method produces trees for final comparison using reconciliation methods, but it includes only as many incongruence events as can be statistically justified from the data sets. We apply this method to a host–parasite (gopher–louse) data set and identify many fewer incongruence events than do topology based analyses alone. Our method is broadly applicable to comparisons of phylogenies of interacting taxa, such as hosts and parasites, or mutualists. The method should also be useful for other problems involving comparisons of phylogenies, such as multiple gene trees or cladistic biogeography.

Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny

Paralogy is a pervasive problem in trying to use nuclear gene sequences to infer species phylogenies. One strategy for dealing with this problem is to infer species phylogenies from gene trees using reconciled trees, rather than directly from the sequences themselves. In this approach, the optimal species tree is the tree that requires the fewest gene duplications to be invoked. Because reconciled trees can identify orthologous from paralogous sequences, there is no need to do this prior to the analysis. Multiple gene trees can be analyzed simultaneously; however, the problem of nonuniform gene sampling raises practical problems which are discussed. In this paper the technique is applied to phylogenies for nine vertebrate genes (aldolase, α-fetoprotein, lactate dehydrogenase, prolactin, rhodopsin, trypsinogen, tyrosinase, vassopressin, and Wnt-7). The resulting species tree shows much similarity with currently accepted vertebrate relationships.

Trees within trees: genes and species, molecules and morphology.

The construction and interpretation of gene trees is fundamental in molecular systematics. If the gene is defined in a historical (coalescent) sense, there can be multiple gene trees within the single contiguous set of nucleotides, and attempts to construct a single tree for such a sequence must deal with homoplasy created by conflict among divergent histories. On a larger scale, incongruence is expected among gene tree topologies at different loci of individuals within sexually reproducing species, and it has been suggested that this discordance can be used to delimit species. A practical concern for such topological methods is that polymorphisms may be maintained through numerous cladogenic events; this polymorphism problem is less of a concern for nontopological approaches to species delimitation using molecular data. Although a central theoretical concern in molecular systematics is discordance between a given gene tree and the true "species tree," the primary empirical problem faced in reconstructing taxic phylogeny is incongruence among the trees inferred from different sequences. Linkage relationships limit character independence and thus have important implications for handling multiple data sets in phylogenetic analysis, particularly at the species level, where incongruence among different historically associated loci is expected. Gene trees can also be reconstructed for loci that influence phenotypic characters, but there is at best a tenuous relationship between phenotypic homoplasy and homoplasy in such gene trees. Nevertheless, expression patterns and orthology relationships of genes involved in the expression of phenotypes can in theory provide criteria for homology assessment of morphological characters.