Abstract
BackgroundThe level of nucleotide diversity observed across the genome is positively correlated with the local rate of recombination. Avian karyotypes are typified by large variation in chromosome size and the rate of recombination in birds has been shown to be negatively correlated with chromosome size. It has thus been predicted that nucleotide diversity is negatively correlated with chromosome size in aves. However, there is limited empirical evidence to support this prediction.ResultsHere we sequenced 27 autosomal and 12 sex chromosome-linked loci in the white-throated sparrow (Zonotrichia albicollis) to quantify and compare patterns of recombination, linkage disequilibrium (LD), and genetic diversity across the genome of this North American songbird. Genetic diversity on the autosomes varied up to 8-fold, with the lowest diversity observed on the macrochromosomes and the highest diversity on the microchromosomes. Genetic diversity on the sex chromosomes was reduced compared to the autosomes, the most extreme difference being a ~300-fold difference between the W chromosome and the microchromosomes. LD and population structure associated with a common inversion polymorphism (ZAL2/2m) in this species were found to be atypical compared to other macrochromosomes, and nucleotide diversity within this inversion on the two chromosome arrangements was more similar to that observed on the Z chromosome.ConclusionsA negative correlation between nucleotide diversity and autosome size was observed in the white-throated sparrow genome, as well as low levels of diversity on the sex chromosomes comparable to those reported in other birds. The population structure and extended LD associated with the ZAL2/2m chromosomal polymorphism are exceptional compared to the rest of the white-throated sparrow genome.
Highlights
The level of nucleotide diversity observed across the genome is positively correlated with the local rate of recombination
The unusually high linkage disequilibrium (LD) would make the ZAL2m and the ZAL2 sensitive to HRI and, in a previous study [22], we found genetic diversity within the inversion region on both arrangements to be reduced relative to the region outside the inversion
Patterns of nucleotide diversity To understand patterns of diversity as they relate to chromosome size, we grouped our autosomal data into three categories: macrochromosomes, intermediate chromosomes, and microchromosomes
Summary
The level of nucleotide diversity observed across the genome is positively correlated with the local rate of recombination. Background selection and genetic hitchhiking reduce overall levels of variation and inhibit the efficacy of selection because selection cannot act on mutations independently as a result of LD. This phenomenon is known as Hill-Robertson Interference or HRI [6]. Levels of nucleotide diversity are positively correlated with local rates of recombination [7] which are known to be variable across a genome [8]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
