15,060 research outputs found
Synthesizing species trees from gene trees using the parameterized and graph-theoretic approaches
Gene trees describe how parts of the species have evolved over time, and it is assumed that gene trees have evolved along the branches of the species tree. However, some of gene trees are often discordant with the corresponding species tree due to the complicated evolution history of genes. To overcome this obstacle, median problems have emerged as a major tool for synthesizing species trees by reconciling discordance in a given collection of gene trees. Given a collection of gene trees and a cost function, the median problem seeks a tree, called median tree, that minimizes the overall cost to the gene trees. Median tree problems are typically NP-hard, and there is an increased interest in making such median tree problems available for large-scale species tree construction.
In this thesis work, we first show that the gene duplication median tree problem satisfied the weaker version of the Pareto property and propose a parameterized algorithm to solve the gene duplication median tree problem. Second, we design two efficient methods to handle the issues of applying the parameterized algorithm to unrooted gene trees which are sampled from the different species. Third, we introduce the graph-theoretic formulation of the Robinson-Foulds median tree problem and a new tree edit operation. Fourth, we propose a new metric between two phylogenetic trees and examine the statistical properties of the metric. Finally, we propose a new clustering criteria in a bipartite network and propose a new NP-hard problem and its ILP formulation
Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication
Horseshoe crabs are marine arthropods with a fossil record extending back
approximately 450 million years. They exhibit remarkable morphological
stability over their long evolutionary history, retaining a number of ancestral
arthropod traits, and are often cited as examples of "living fossils." As
arthropods, they belong to the Ecdysozoa}, an ancient super-phylum whose
sequenced genomes (including insects and nematodes) have thus far shown more
divergence from the ancestral pattern of eumetazoan genome organization than
cnidarians, deuterostomes, and lophotrochozoans. However, much of ecdysozoan
diversity remains unrepresented in comparative genomic analyses. Here we use a
new strategy of combined de novo assembly and genetic mapping to examine the
chromosome-scale genome organization of the Atlantic horseshoe crab Limulus
polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by
sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their
parents at a mean redundancy of 1.1x per sample. The map includes 84,307
sequence markers and 5,775 candidate conserved protein coding genes. Comparison
to other metazoan genomes shows that the L. polyphemus genome preserves
ancestral bilaterian linkage groups, and that a common ancestor of modern
horseshoe crabs underwent one or more ancient whole genome duplications (WGDs)
~ 300 MYA, followed by extensive chromosome fusion
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
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