Comparative genomics reveals insights into avian genome evolution and adaptation

Abstract

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

“…The net frequency of nucleotide substitutions (d A ) was calculated according to the method of Nei 48 , and the time since divergence (t) of alleles was calculated as t = d A /2λ, where λ is the genomic substitution rate. As a substitution rate in ruff is not yet available, we used the substitution rates estimated for each of 48 other bird genomes 18 to calculate a confidence interval for t, and the data are presented as a box plot.…”

Visual pigments in a palaeognath bird, the emuDromaius novaehollandiae: implications for spectral sensitivity and the origin of ultraviolet vision

“…The four single cones generate a tetrachromatic visual system capable of excellent colour discrimination across the visible spectrum [33], and this is further refined by the presence of pigmented oil droplets that filter incoming light [34,35]. The only exceptions to this general format appear in some species of penguin, which have lost their MWS cone visual pigment through pseudogenization of the RH2 opsin gene [36] and appear to possess only three spectral types of single cone [37]. Molecular analysis of the emu retina confirmed the expression of a single rod and four cone opsin genes, which accounts for the observed spectral characteristics of the different cone and rod photoreceptors.…”

Linkage mapping of a polymorphic plumage locus associated with intermorph incompatibility in the Gouldian finch (Erythrura gouldiae)

“…Many avian species share highly conserved synteny, but with various degrees of intrachromosomal rearrangement (Kawakami et al, 2014;Zhang et al, 2014). For example, no genomic rearrangements were found in the sex chromosomes between closely related Ficedula flycatcher species (Backström et al, 2010b), whereas there are karyotypic polymorphisms on the Z chromosome in ZF (Itoh et al, 2011) and an inversion is associated with alternative reproductive morphs in the ruff (Küpper et al, 2016;Lamichhaney et al, 2016).…”