10,484 research outputs found
Network Archaeology: Uncovering Ancient Networks from Present-day Interactions
Often questions arise about old or extinct networks. What proteins interacted
in a long-extinct ancestor species of yeast? Who were the central players in
the Last.fm social network 3 years ago? Our ability to answer such questions
has been limited by the unavailability of past versions of networks. To
overcome these limitations, we propose several algorithms for reconstructing a
network's history of growth given only the network as it exists today and a
generative model by which the network is believed to have evolved. Our
likelihood-based method finds a probable previous state of the network by
reversing the forward growth model. This approach retains node identities so
that the history of individual nodes can be tracked. We apply these algorithms
to uncover older, non-extant biological and social networks believed to have
grown via several models, including duplication-mutation with complementarity,
forest fire, and preferential attachment. Through experiments on both synthetic
and real-world data, we find that our algorithms can estimate node arrival
times, identify anchor nodes from which new nodes copy links, and can reveal
significant features of networks that have long since disappeared.Comment: 16 pages, 10 figure
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
Developmental constraints on vertebrate genome evolution
Constraints in embryonic development are thought to bias the direction of
evolution by making some changes less likely, and others more likely, depending
on their consequences on ontogeny. Here, we characterize the constraints acting
on genome evolution in vertebrates. We used gene expression data from two
vertebrates: zebrafish, using a microarray experiment spanning 14 stages of
development, and mouse, using EST counts for 26 stages of development. We show
that, in both species, genes expressed early in development (1) have a more
dramatic effect of knock-out or mutation and (2) are more likely to revert to
single copy after whole genome duplication, relative to genes expressed late.
This supports high constraints on early stages of vertebrate development,
making them less open to innovations (gene gain or gene loss). Results are
robust to different sources of data-gene expression from microarrays, ESTs, or
in situ hybridizations; and mutants from directed KO, transgenic insertions,
point mutations, or morpholinos. We determine the pattern of these constraints,
which differs from the model used to describe vertebrate morphological
conservation ("hourglass" model). While morphological constraints reach a
maximum at mid-development (the "phylotypic" stage), genomic constraints appear
to decrease in a monotonous manner over developmental time
- âŠ