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All figures (10)
Figure 2. Unrooted neighbour-joining tree of Emberizidae species constructed based on average absolute between-population nucleotide diversity (!!). Sample sizes for each species are as follows: E. aureola = 1, E. calandra = 1, E. cioides = 1, E. hortulana = 1, E. cirlus = 6, E. stewarti = 4, E. citrinella = 53 and E. leucocephalos = 42.
Table 2. Summary statistics calculated while conducting mitonuclear co-introgression analysis. A total of 7187 windows, each of 2000 bp of obtained sequence, were considered when determining introgression windows. A total of 134 mitonuclear genes were investigated for signals of co-introgression. “*” indicates a significant p-value.
Figure 6. Mean absolute within-group nucleotide diversity (!") of allopatric yellowhammers (n = 53) and allopatric pine buntings (n =42) plotted against absolute between-group nucleotide diversity (!!). Each dot represents the average value taken from a 2000 bp window of sequenced data across the nuclear genome. The black line indicates where mean within-group nucleotide diversity equals between-group nucleotide diversity. Increasing values of relative differentiation (FST) calculated for each window are shown in darker shades of blue.
Table 3. Identities, chromosomal locations, windowed Tajima’s D values and functions of mitonuclear genes that appeared within 244 yellowhammer introgression windows. In the “Mitonuclear Gene Function” column, ETC stands for “Electron Transport Chain”. Mitonuclear gene names are written as they appear in Hill (2019).
Figure 5. Patterns of genetic variation comparing allopatric yellowhammers (n = 53) and allopatric pine buntings (n = 42) across three chromosomes (2, 5 and Z). Relative nucleotide differentiation (FST), absolute between-population nucleotide diversity (!!), absolute withinpopulation nucleotide diversity (!") and Tajima’s D (TajD) are shown as 2000 bp windowed averages across each chromosome. FST and !! are shown as purple lines to indicate that values were calculated as a comparison between allopatric yellowhammers and pine buntings. !" and TajD are shown as two separate lines (yellow = yellowhammers, brown = pine buntings) to indicate that values were calculated separately for each population.
Figure 4. Relative differentiation (FST) of 349,807 genome-wide SNPs identified between allopatric yellowhammers (n = 53) and allopatric pine buntings (n = 42), with chromosomes represented with alternating black and grey. Narrow regions of elevated differentiation can be seen on many autosomes, and there are broad regions of high differentiation on the Z chromosome.
Table 4. Identities, chromosomal locations, windowed Tajima’s D values and functions of mitonuclear genes that appeared within 222 pine bunting introgression windows. In the “Mitonuclear Gene Function” column, ETC stands for “Electron Transport Chain”. Mitonuclear gene names are written as they appear in Hill (2019).
Figure 3. PCA of genetic variation between allopatric yellowhammers (yellow; n = 53) and allopatric pine buntings (brown; n = 42), based on 374,780 genome-wide SNPs. PC1 and PC2 explain 3.6% and 2.9%, respectively, of the variation among individuals.
Table 1. Geographical locations and sample sizes of the sites included in this study. Sampling locations may include multiple sites that appeared too close together to be shown in detail in Figure 1A. Full details for the sites included in each sampling locations can be found in Supplementary Table 1. The sampling location numbers that appear in the “Sampling Location” column correspond to those that appear in red in Figure 1A. The “Sample Size” columns describes the total number of samples collected from a particular location.
Figure 7. Association between relative differentiation (FST) and absolute between-group nucleotide diversity (!!) of allopatric yellowhammers (n=53) and allopatric pine buntings (n = 42). Each black dot represents average values calculated from a 2000 bp window of sequenced data. A cubic spline fit between the variables is shown as a purple line.
Posted Content
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DOI
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Mitonuclear co-introgression opposes genetic differentiation between phenotypically divergent songbirds
[...]
Ellen Nikelski
1
,
A. S. Rubtsov
,
Darren E. Irwin
2
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Institutions (2)
University of Toronto
1
,
University of British Columbia
2
08 Aug 2021
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bioRxiv