43,557 research outputs found
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
A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements
Ray-finned fishes constitute the dominant radiation of vertebrates with over
30,000 species. Although molecular phylogenetics has begun to disentangle major
evolutionary relationships within this vast section of the Tree of Life, there
is no widely available approach for efficiently collecting phylogenomic data
within fishes, leaving much of the enormous potential of massively parallel
sequencing technologies for resolving major radiations in ray-finned fishes
unrealized. Here, we provide a genomic perspective on longstanding questions
regarding the diversification of major groups of ray-finned fishes through
targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their
flanking sequence. Our workflow efficiently and economically generates data
sets that are orders of magnitude larger than those produced by traditional
approaches and is well-suited to working with museum specimens. Analysis of the
UCE data set recovers a well-supported phylogeny at both shallow and deep
time-scales that supports a monophyletic relationship between Amia and
Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be
the earliest diverging teleost lineages. Divergence time estimation based upon
14 fossil calibrations reveals that crown teleosts appeared ~270 Ma at the end
of the Permian and that elopomorphs, osteoglossomorphs, ostarioclupeomorphs,
and euteleosts diverged from one another by 205 Ma during the Triassic. Our
approach additionally reveals that sequence capture of UCE regions and their
flanking sequence offers enormous potential for resolving phylogenetic
relationships within ray-finned fishes
Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium
Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres
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