Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

Abstract

With methods for sequencing thousands of loci for many individuals, phylogeographic studies have increased inferential power and the potential for applications to new questions. In songbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the ability to obtain thousands of genetic loci for many individuals permit the investigation of differentiation between and diversity within lineages across chromosomes. Here, we investigate patterns of differentiation and diversity in Certhia americana, a widespread North American songbird, using next-generation sequencing. Additionally, we reassess previous phylogeographic studies within the group. Based on~30 million sequencing reads and more than 16 000 single-nucleotide polymorphisms in 41 individuals, we identified a strong positive relationship between genetic differentiation and chromosome size, with a negative relationship between genetic diversity and chromosome size. A combination of selection and drift may explain these patterns, although we found no evidence for selection. Because the observed genomic patterns are very similar between widespread, allopatric clades, it is unlikely that selective pressures would be so similar across such different ecological conditions. Alternatively, the accumulation of fixed differences between lineages and loss of genetic variation within lineages due to genetic drift alone may explain the observed patterns. Due to relatively higher recombination rates on smaller chromosomes, larger chromosomes would, on average, accumulate fixed differences between lineages and lose genetic variation within lineages faster, leading to the patterns observed here in C. americana.

Comparison of the genetic relationship between nine Cephalopod species based on cluster analysis of karyotype evolutionary distance

“…Arslan and Zima (2015) also emphasized that a cytotype may include several populations with different karyotypes despite having the same diploid number of chromosomes. Similarly, chromosomal diversity and differentiation has been confirmed in creepers (Manthey et al 2015). In addition, the present study revealed a new karyotype of O. minor which was clearly different from results of Inaba (1959), who reported a diploid chromosome number of 56 in spermatogonia and primary spermatocytes.…”

Can genomic variation explain the extinction of the passenger pigeon?

“…The π values at the edges of chromosomes were up to ten-fold higher than other parts of chromosomes ( Fig. 2B of Murray et al 2017), which exceed differences found in other studies (Manthey et al 2015). The results imply that parts of their estimated SNPs can be imprecise.…”

“…In contrast, we believe that low genomic mapping quality at the edges of chromosomes in the passenger pigeon is a more likely reason. If high recombination rates at the edges of chromosomes are the reason, we should find similar patterns in the genomes of the band-tailed pigeon or other avian species; however, it is not the case (Ellegren et al 2012; but see Manthey et al 2015). Even though Murray et al (2017) took some measurements to reduce the potential impacts of postmortem DNA damages on mapping and SNP calling, the efficiency of their approaches seems limited given the observed pattern.…”

“…Murray et al (2017) showed the highly variable and uneven distribution of genetic polymorphism across the passenger pigeon genome and used it as evidence of natural selection. However, the uneven genetic polymorphism landscape does not necessarily reflect the impact of natural selection in the genome because genetic drift can also cause such a pattern (Manthey et al 2015). The π values at the edges of chromosomes were up to ten-fold higher than other parts of chromosomes ( Fig.…”

Conservation genomics reveals multiple evolutionary units within Bell’s Vireo (Vireo bellii)

“…Genomic methods offer a promising tool for conservation genetics and are quickly becoming a common method for obtaining numerous loci for multiple individuals in phylogenetic and phylogeographic studies (Manthey et al 2015). However, distinguishing the roles of dispersal, vicariance, and gene flow in explaining population structure continues to be a challenge.…”