2,697 research outputs found
Unifying Parsimonious Tree Reconciliation
Evolution is a process that is influenced by various environmental factors,
e.g. the interactions between different species, genes, and biogeographical
properties. Hence, it is interesting to study the combined evolutionary history
of multiple species, their genes, and the environment they live in. A common
approach to address this research problem is to describe each individual
evolution as a phylogenetic tree and construct a tree reconciliation which is
parsimonious with respect to a given event model. Unfortunately, most of the
previous approaches are designed only either for host-parasite systems, for
gene tree/species tree reconciliation, or biogeography. Hence, a method is
desirable, which addresses the general problem of mapping phylogenetic trees
and covering all varieties of coevolving systems, including e.g., predator-prey
and symbiotic relationships. To overcome this gap, we introduce a generalized
cophylogenetic event model considering the combinatorial complete set of local
coevolutionary events. We give a dynamic programming based heuristic for
solving the maximum parsimony reconciliation problem in time O(n^2), for two
phylogenies each with at most n leaves. Furthermore, we present an exact
branch-and-bound algorithm which uses the results from the dynamic programming
heuristic for discarding partial reconciliations. The approach has been
implemented as a Java application which is freely available from
http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
The inference of gene trees with species trees
Molecular phylogeny has focused mainly on improving models for the
reconstruction of gene trees based on sequence alignments. Yet, most
phylogeneticists seek to reveal the history of species. Although the histories
of genes and species are tightly linked, they are seldom identical, because
genes duplicate, are lost or horizontally transferred, and because alleles can
co-exist in populations for periods that may span several speciation events.
Building models describing the relationship between gene and species trees can
thus improve the reconstruction of gene trees when a species tree is known, and
vice-versa. Several approaches have been proposed to solve the problem in one
direction or the other, but in general neither gene trees nor species trees are
known. Only a few studies have attempted to jointly infer gene trees and
species trees. In this article we review the various models that have been used
to describe the relationship between gene trees and species trees. These models
account for gene duplication and loss, transfer or incomplete lineage sorting.
Some of them consider several types of events together, but none exists
currently that considers the full repertoire of processes that generate gene
trees along the species tree. Simulations as well as empirical studies on
genomic data show that combining gene tree-species tree models with models of
sequence evolution improves gene tree reconstruction. In turn, these better
gene trees provide a better basis for studying genome evolution or
reconstructing ancestral chromosomes and ancestral gene sequences. We predict
that gene tree-species tree methods that can deal with genomic data sets will
be instrumental to advancing our understanding of genomic evolution.Comment: Review article in relation to the "Mathematical and Computational
Evolutionary Biology" conference, Montpellier, 201
Exact reconciliation of undated trees
Reconciliation methods aim at recovering macro evolutionary events and at
localizing them in the species history, by observing discrepancies between gene
family trees and species trees. In this article we introduce an Integer Linear
Programming (ILP) approach for the NP-hard problem of computing a most
parsimonious time-consistent reconciliation of a gene tree with a species tree
when dating information on speciations is not available. The ILP formulation,
which builds upon the DTL model, returns a most parsimonious reconciliation
ranging over all possible datings of the nodes of the species tree. By studying
its performance on plausible simulated data we conclude that the ILP approach
is significantly faster than a brute force search through the space of all
possible species tree datings. Although the ILP formulation is currently
limited to small trees, we believe that it is an important proof-of-concept
which opens the door to the possibility of developing an exact, parsimony based
approach to dating species trees. The software (ILPEACE) is freely available
for download
Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance
We present a new method for inferring species trees from multi-copy gene
trees. Our method is based on a generalization of the Robinson-Foulds (RF)
distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple
leaves can have the same label. Unlike most previous phylogenetic methods using
gene trees, this method does not assume that gene tree incongruence is caused
by a single, specific biological process, such as gene duplication and loss,
deep coalescence, or lateral gene transfer. We prove that it is NP-hard to
compute the RF distance between two mul-trees, but it is easy to calculate the
generalized RF distance between a mul-tree and a singly-labeled tree. Motivated
by this observation, we formulate the RF supertree problem for mul-trees
(MulRF), which takes a collection of mul-trees and constructs a species tree
that minimizes the total RF distance from the input mul-trees. We present a
fast heuristic algorithm for the MulRF supertree problem. Simulation
experiments demonstrate that the MulRF method produces more accurate species
trees than gene tree parsimony methods when incongruence is caused by gene tree
error, duplications and losses, and/or lateral gene transfer. Furthermore, the
MulRF heuristic runs quickly on data sets containing hundreds of trees with up
to a hundred taxa.Comment: 16 pages, 11 figure
2× genomes - depth does matter
The use of low coverage genomes in comparative evolutionary analyses skews estimates of gene gains and losses
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