Predicting the ancestral character changes in a tree is typically easier than predicting the root state
Olivier Gascuel, Mike Steel
(Submitted on 4 Sep 2013)

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show that when the mutation rate become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show that, depending on the tree and branch length distribution, reconstructing these changes (i.e. reconstructing the ancestral state of all internal nodes in the tree) may be easier or harder than reconstructing the ancestral root state. However, results from information theory indicate that for the standard Yule tree, the task of reconstructing internal node states remains feasible, even for very high substitution rates. Moreover, computer simulations demonstrate that for more complex trees and scenarios, this result still holds. For a large variety of counting, parsimony-based and likelihood-based methods, the predictive accuracy of a randomly selected internal node in the tree is indeed much higher than the accuracy of the same method when applied to the tree root. Moreover, parsimony- and likelihood-based methods appear to be remarkably robust to sampling bias and model mis-specification.

Target capture and massively parallel sequencing of ultraconserved elements (UCEs) for comparative studies at shallow evolutionary time scales
Brian Tilston Smith, Michael G. Harvey, Brant C. Faircloth, Travis C. Glenn, Robb T. Brumfield
(Submitted on 24 Aug 2013)

Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species, we recovered 776-1,516 UCE loci across the five species. Across species, 53-77 percent of the loci were polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic locus, on average. We performed species tree construction, coalescent modeling, and species delimitation, and we found that the five co-distributed species exhibited discordant phylogeographic histories. We also found that species trees and divergence times estimated from UCEs were similar to those obtained from mtDNA. The species that inhabit the understory had older divergence times across barriers, contained a higher number of cryptic species, and exhibited larger effective population sizes relative to species inhabiting the canopy. Because orthologous UCEs can be obtained from a wide array of taxa, are polymorphic at shallow evolutionary time scales, and can be generated rapidly at low cost, they are effective genetic markers for studies investigating evolutionary patterns and processes at shallow time scales.

Macro-evolutionary models and coalescent point processes: The shape and probability of reconstructed phylogenies
Amaury Lambert, Tanja Stadler
(Submitted on 6 Aug 2013)

Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow “vertically” as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees (i.e., phylogenies of extant species). Alternatively, reconstructed trees can be modelled by coalescent point processes (CPP), where trees grow “horizontally” by the sequential addition of vertical edges. Each new edge starts at some random speciation time and ends at the present time; speciation times are drawn from the same distribution independently. CPP lead to extremely fast computation of tree likelihoods and simulation of reconstructed trees. Their topology always follows the uniform distribution on ranked tree shapes (URT). We characterize which forward-time models lead to URT reconstructed trees and among these, which lead to CPP reconstructed trees. We show that for any “asymmetric” diversification model in which speciation rates only depend on time and extinction rates only depend on time and on a non-heritable trait (e.g., age), the reconstructed tree is CPP, even if extant species are incompletely sampled. If rates additionally depend on the number of species, the reconstructed tree is (only) URT (but not CPP). We characterize the common distribution of speciation times in the CPP description, and discuss incomplete species sampling as well as three special model cases in detail: 1) extinction rate does not depend on a trait; 2) rates do not depend on time; 3) mass extinctions may happen additionally at certain points in the past.

An Arrow-type result for inferring a species tree from gene trees
Mike Steel
(Submitted on 19 Jul 2013)

The reconstruction of a central tendency `species tree’ from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all taxa are present in every gene tree. Here, we list four desirable properties that a method for estimating a species tree from gene trees should have. We show that while these can be achieved when taxon coverage is complete (by the Adams consensus method), they cannot all be satisfied in the more general setting of partial taxon coverage.