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Posterior probability plots of bi-directional migration rates (given in effective number of gene copies - 2Nm) estimated between Icterus bullockii and I. galbula (a,d), between I. abeillei and I. bullockii (b,e), and between I. abeillei and I. galbula (c,f) based on a combined three-population analysis and three separate pairwise analyses in IMa2.

Posterior probability plots of bi-directional migration rates (given in effective number of gene copies - 2Nm) estimated between Icterus bullockii and I. galbula (a,d), between I. abeillei and I. bullockii (b,e), and between I. abeillei and I. galbula (c,f) based on a combined three-population analysis and three separate pairwise analyses in IMa2.

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Until recently, studies of divergence and gene flow among closely-related taxa were generally limited to pairs of sister taxa. However, organisms frequently exchange genes with other non-sister taxa. The "northern oriole" group within genus Icterus exemplifies this problem. This group involves the extensively studied hybrid zone between Baltimore o...

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... inclusion of all three members of this species com- plex in a single IMa2 analysis revealed some interesting patterns of gene introgression (Fig. 4). The two compet- ing population trees (nDNA vs. mtDNA) yielded similar parameter estimates (with one important exception dis- cussed below). We therefore only report the results based on the nuclear population tree (I. galbula, (I. abeillei, I. ...
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... we found clear evidence of substantial introgression across the hybrid zone between I. galbula and I. bullockii, (2Nm I. galbula > I. bullockii = 3.388, 95% HPD = 0.41-12.30, vs. 2Nm I. bullockii > I. galbula = 2.125, 95% HPD = 0.193- 6.504, Fig. 4a). Interestingly, the gene flow appears to be slightly skewed in the direction of I. bullockii. In contrast, we did not detect any gene flow between the sister species I. bullockii (Fig. 4b). The gene flow estimates virtually peaked at zero (2Nm = 0.001 in both directions) and the 95% HPD intervals ranged from 0 to 1.148 and 0 to 0.495 ...
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... I. galbula and I. bullockii, (2Nm I. galbula > I. bullockii = 3.388, 95% HPD = 0.41-12.30, vs. 2Nm I. bullockii > I. galbula = 2.125, 95% HPD = 0.193- 6.504, Fig. 4a). Interestingly, the gene flow appears to be slightly skewed in the direction of I. bullockii. In contrast, we did not detect any gene flow between the sister species I. bullockii (Fig. 4b). The gene flow estimates virtually peaked at zero (2Nm = 0.001 in both directions) and the 95% HPD intervals ranged from 0 to 1.148 and 0 to 0.495 in the direction of I. bullockii and I. abeillei, respectively. Similarly, the three-population analysis did not detect any gene flow between the highly allopatric I. galbula and I. abeillei ...
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... (Fig. 4b). The gene flow estimates virtually peaked at zero (2Nm = 0.001 in both directions) and the 95% HPD intervals ranged from 0 to 1.148 and 0 to 0.495 in the direction of I. bullockii and I. abeillei, respectively. Similarly, the three-population analysis did not detect any gene flow between the highly allopatric I. galbula and I. abeillei (Fig. 4c), with gene flow estimates peaking near zero and 95% HPD intervals ranging from 0 to 0.631 and 0 to 0.719 in the direction of I. galbula and I. abeillei, respectively. There was no evidence of historical gene flow between the I. galbula lineage and the ancestral I. abeillei/ I. bullockii ...
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... is presented in Table 3. Estimates of gene flow were mostly consistent between the pairwise two-population analyses and the three-population analysis. However, the two-population analysis of I. abeillei and I. galbula sug- gested a small but significant amount of introgression from I. abeillei into I. galbula (2Nm I. abeillei > I. galbula = 0.477 (Fig. 4f). Although the 95% HPD interval included zero (see Table 5), nested model testing conducted in IMa2 indicated that a reduced model with zero migration was a significantly worse fit to the data than the full model allowing for migration (results not ...
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... the two-population analysis of I. galbula and I. bullockii indicated lower but equal rates of intro- gression in both directions (2Nm I. bullockii > I. galbula = 1.331 and 2Nm I. galbula > I. bullocki = 1.275, see Fig. ...

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... We detected secondary gene flow between stricklandii from Sabah and the eastern Javan clade ( fig. 1), even though they are distantly related in the complex, adding to previous insights that secondary gene flow does not necessarily have to be restricted to sister lineages (Dasmahapatra et al. 2012;Jacobsen and Omland 2012;Edelman et al. 2019;Gwee et al. 2020). ...
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Chapter
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Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits. Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species. Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow.
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