Evidence for Strong Fixation Bias at 4-fold Degenerate Sites Across Genes in the Great Tit Genome
Permanent link
https://hdl.handle.net/10037/14810Date
2018-11-29Type
Journal articleTidsskriftartikkel
Peer reviewed
Author
Gossmann, Toni Ingolf; Bockwoldt, Mathias; Diringer, Lilith; Schwarz, Friedrich; Schumann, Vic-FabienneAbstract
It is well established that GC content varies across the genome in many species
and that GC biased gene conversion, one form of meiotic recombination, is likely to
contribute to this heterogeneity. Bird genomes provide an extraordinary system to study
the impact of GC biased gene conversion owed to their specific genomic features. They
are characterized by a high karyotype conservation with substantial heterogeneity in
chromosome sizes, with up to a dozen large macrochromosomes and many smaller
microchromosomes common across all bird species. This heterogeneity in chromosome
morphology is also reflected by other genomic features, such as smaller chromosomes
being gene denser, more compact and more GC rich relative to their macrochromosomal
counterparts - illustrating that the intensity of GC biased gene conversion varies across
the genome. Here we study whether it is possible to infer heterogeneity in GC biased gene
conversion rates across the genome using a recently published method that accounts
for GC biased gene conversion when estimating branch lengths in a phylogenetic
context. To infer the strength of GC biased gene conversion we contrast branch length
estimates across the genome both taking and not taking non-stationary GC composition
into account. Using simulations we show that this approach works well when GC
fixation bias is strong and note that the number of substitutions along a branch is
consistently overestimated when GC biased gene conversion is not accounted for. We
use this predictable feature to infer the strength of GC dynamics across the great tit
genome by applying our new pipeline to data at 4-fold degenerate sites from three
bird species—great tit, zebra finch and chicken—three species that are among the best
annotated bird genomes to date. We show that using a simple one-dimensional binning
we fail to capture a signal of fixation bias as observed in our simulations. However, using
a multidimensional binning strategy, we find evidence for heterogeneity in the strength
of fixation bias, including AT fixation bias. This highlights the difficulties when combining
sequence data across different regions in the genome.
Description
Source at https://doi.org/10.3389/fevo.2018.00203.