SNP_dataset_for_Dryad

SNP dat

Support for latitude versus presence or absence of song learning and year-round territoriality as drivers of song response evolution.

Song response is modeled as a function of genetic distance using the Michaelis–Menten framework. The “allopatric” dataset includes allopatric and parapatric taxon pairs but excludes 20 sister pairs that occur in sympatry.</p

Song playbacks demonstrate slower evolution of song discrimination in birds from Amazonia than from temperate North America - Fig 2

Song discrimination for Amazonian (red) and high latitude North American (blue) taxon pairs with at least two playback experiments performed. Excluding experiments with only a single playback experiment reduced the scatter but had limited impact on the best-fit relationship. The best-fit Michaelis–Menten curves and their 95% confidence bands are shown, calculated as in Fig 1A (statistics are in S2 Table). Intraspecific (open inverted triangles) and species-level (solid triangles) splits are shown separately. Yellow lines highlight selected intraspecific splits with discrimination scores exceeding 0.7. Green lines highlight selected allopatric or parapatric species-level splits with discrimination scores less than 0.3. Sonograms for highlighted taxon pairs plot song frequency (y axis, with each bar representing an increase of 2 kilohertz) versus time (x axis, with time shown at the same scale within a taxon pair but not between them), with warmer colors representing higher amplitude. Photos were taken from Flickr (www.flickr.com) under the CC-BY 2.0 license. Photo credits as follows. Common Yellowthroat: left, synspectrum; right, Andy Morffew. Hermit Thrush: left, Becky Matsubara; right, Matt McGillivray. Marsh Wren: left, Nigel; right, Andy Reago and Crissy McClarren. Playback data used to make this figure are in S1 Data. CC, Creative Commons.</p

Supporting Information

Appendix S1. References of molecular phylogenetic studies used to identify the sister pairs in our data set. Loadings of PCA results. Results of model fitting. Appendix S2. GenBank accession numbers. Appendix S3. Elevational differentiation (meters) and Euclidean distances of morphometrics and song measurements (PCs). Fig. S1. Phylogeny of the sister species pairs included in our data set. Color range indicates the degree of elevational differentiation in the left phylogeny and the amount of overlap in the right phylogeny.Fig. S2. Example of measurements taken from song spectrograms.Fig. S3. Example of morphological measurements taken from museum specimens. </div

Song playbacks demonstrate slower evolution of song discrimination in birds from Amazonia than from temperate North America - Fig 1

Comparison of song discrimination in Amazonia (red or red and green) versus high latitudes of North America (blue). (A) Song discrimination as a function of genetic distance with separate Michaelis–Menten curves applied to Amazonia and temperate regions. Expectations (solid lines) and 95% confidence bands (shading) obtained from 1,000 bootstrap replicates in which only a single taxon pair was sampled from within each species complex (see S5 Fig). Sympatric taxa pairs that were excluded from analyses using only non-sympatric taxa (see Table 1) are outlined in black. (B) is the same as in A, but with curves for Amazonian species in which year-round territoriality is present (red) or absent (green). (C) and (D) are the same as in A and B, except that song discrimination is a function of a composite of song frequency and length divergence (using Euclidean distance of PC1 to PC3 for our PCA of all song measures) using a Michaelis–Menten curve with intercept free to vary (Eq 4). Though confidence bands overlap across bootstraps in some of these analyses, discrimination was greater in the temperate than Amazonia in 100% of bootstrap replicates for (A), 97.6% for (B), 99.9% for (C), and 95.1% for (D). Data used to make this figure are in S1 Data. PC, principal component; PCA, principal component analysis.</p

R code triangle plot simulations from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

We possess limited understanding of how speciation unfolds in the most species rich region of the planet—the Amazon basin. Hybrid zones provide valuable information on the evolution of reproductive isolation, but few studies of Amazonian vertebrate hybrid zones have rigorously examined the genome-wide underpinnings of reproductive isolation. We used genome-wide genetic datasets to show that two deeply diverged, but morphologically cryptic sister species of forest understory birds show little evidence for prezygotic reproductive isolation, but substantial postzygotic isolation. Patterns of heterozygosity and hybrid index revealed that hybrid classes with heavily recombined genomes are rare and closely match simulations with high levels of selection against hybrids. Genomic and geographical clines exhibit a remarkable similarity across loci in cline centres, and have exceptionally narrow cline widths, suggesting that postzygotic isolation is driven by genetic incompatibilities at many loci, rather than a few loci of strong effect. We propose Amazonian understory forest birds speciate slowly via gradual accumulation of postzygotic genetic incompatibilities, with prezygotic barriers playing a less important role. Our results suggest many cryptic Amazonian taxa classified as subspecies could have substantial postzygotic isolation deserving species recognition and that species richness is likely to be substantially underestimated in Amazonia

Database S1 from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

Willisornis sample detail

Supporting Online Methods and Figures from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

Additional details of methods and result

Supporting Material - Molecular Ecology

The following data corresponds to the Supplemental Information of 'Distinguishing genomic homogenization from parapatric speciation in an elevationally replacing pair of Ramphocelus tanagers'. Appendix S1:Table S1: Pairwise Hudson's FST between populations.Table S2: Results of cline model testing in HZAR for genome-wide hybrid index and two datasets of plumage colouration score, reflectance peak and red proportion in a feather.Table S3: Blast results of overlapping and nearby genes found at the genomic regions of high FST between parental populations.Table S4: Parameter estimates and 95% confidence intervals of best fit demographic model (model 2, Fig. 4). Table S5: Summary of SNP datasets included in our analyses.Figure S1: 0.5 isocline of the hybrid zone.Figure S2: Best fit model of geographic clines of mean proportion of each feather colouration scores along the transect.Figure S3: An example of plumage colouration differentiation between parental and hybrid populations for the rump patch.Figure S4: Genome-wide association with plumage colouration scores.Figure S5: ADMIXTURE’s cross-validation scores for 6 different K clusters across all individuals of the hybrid zone.Appendix S2: Results of GWAS.Appendix S3: Sample information.Appendix S4: Results of song analysis.Input files: Input files used for demographic modelling in fastsimcoal2.</div

Database S2 from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

Xiphorhynchus sample detail