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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
TLDR
A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.
The genome of a songbird
TLDR
This work shows that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets and shows evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience.
The genomic landscape of species divergence in Ficedula flycatchers
TLDR
This study provides a roadmap to the emerging field of speciation genomics by showing that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 ‘divergence islands’ showing up to 50-fold higher sequence divergence than the genomic background.
A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
TLDR
It is found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event per chromosome have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution.
Genomics of natural bird populations: a gene‐based set of reference markers evenly spread across the avian genome
TLDR
A genome‐wide reference set of conserved avian gene markers, broadly applicable across birds, identified by aligning protein‐coding sequences from the recently assembled chicken genome with orthologous sequences in zebra finch to find particularly conserved exonic regions flanking introns of suitable size for subsequent amplification and sequencing.
The recombination landscape of the zebra finch Taeniopygia guttata genome.
TLDR
A positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs and levels of linkage disequilibrium were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.
Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution.
TLDR
A highly significant association of both chromosomal rearrangements and CNVs with elevated recombination rates is found, providing support for the notion of recombination-based processes playing a major role in avian genome evolution.
Molecular evolution of genes in avian genomes
TLDR
There was a weak yet significant negative correlation between ω and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution, and these findings set the stage for studies of functional genetics of avian genes.
Limited number of patrilines in horse domestication
TLDR
It is shown that this high degree of polymorphism is not matched by a corresponding patrilinear diversity of the male-specific Y chromosome, consistent with a strong sex-bias in the domestication process, with few stallions contributing genetically to the domestic horse.
Speciation genetics: current status and evolving approaches
TLDR
This review aims at providing an extensive overview of speciation genetics by focusing much of its attention on evolving approaches and introducing promising methodological approaches for future research venues.
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