Data from: Introgression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): population genetic and phylogenetic inferences from genome-wide SNPs

 

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Title Supp_File_1
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Description SUPPLEMENTARY FILE 1. Custom script (‘tetracolor’) by Rafael Maia in R
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Title Supp_File_2
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Description SUPPLEMENTARY FILE 2. Names (FASTA sequence labels) of the chromosome sequences from the zebra finch genome used in this study.
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Title Supp_File_3
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Description SUPPLEMENTARY FILE 3. Tabular BLASTN results for the Zimmerius contigs against the zebra finch genome, retaining only hits with e-value ≤ 1e-20.
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Title Supp_File_6
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Description SUPPLEMENTARY FILE 6. NEXUS file for parsimony analysis in PAUP.
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Title Supp_File_7
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Description SUPPLEMENTARY FILE 7. R script for gene ontology enrichment analysis.
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Title Supp_File_8
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Description SUPPLEMENTARY FILE 8. Estimates of theta for various datasets and priors. Each of 6 datasets was subjected to a set of alpha and beta parameters allowing for different current and ancestral population sizes: (1) a gamma (2,2000) prior (with`q = 0.001) for small population sizes, and (2) a gamma (1,10) prior (with`q = 0.1) for large population sizes. Three datasets (called ‘allLoci’; n = 954 SNPs) include all SNPs called across all individuals (see Methods), while the three remaining datasets (n = 947) have constant heterozygotes removed; in each of these two groups of datasets, the first dataset includes all lineages, while the other two datasets have one lineage (‘southern’ Z. viridiflavus or ‘intermediate’ mosaic birds) removed. Each theta stands for one of the nodes in the tree. Note how thetas are heavily influenced by the prior.
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Title Supp_File_9
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Description SUPPLEMENTARY FILE 9. A summary of the mapped ABBA/BABA contig statistics, produced by running the script in Supplementary File 5.
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Title Supp_File_10
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Description SUPPLEMENTARY FILE 10. Excel file with six sheets showing associations between ABBA and BABA-like sites with gene ontology (GO) terms from the zebra finch genome. The first three sheets refer to ABBA-like sites; the last three sheets refer to BABA-like sites. Sheets 1 and 4 give associations with GO terms related to cellular components (“cc”), sheets 2 and 5 refer to GO terms related to biological processes (“bp”), and sheets 3 and 6 refer to GO terms related to molecular function (“mf”). In each sheet, GO terms are accompanied by the number of zebra finch genes they are annotated to (“annotated”), followed by the number of ABBA or BABA-linked genes they are annotated to (“significant”), followed by the number of ABBA or BABA-linked genes they would be expected to be annotated to by chance (“expected”), followed by the corrected p value for their over-representation in the ABBA or BABA-linked gene set (“corrected”). The only gene set showing significant (p < 0.05) over-representation of any GO term is the ABBA set for cellular components (sheet 1).
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Title Supp_File_4
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Description SUPPLEMENTARY FILE 4. The output from VarScan used as our SNP datafile for downstream analysis.
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Title Supp_File_5.tar
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Description SUPPLEMENTARY FILE 5. Our main analysis script for population genetic and introgression analyses compiled by P.R.W. (requires python 2.6+ and Biopython). Includes all required accompanying data files. Best run interactively.
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Title zimmerius_prg.fasta
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Description This is the Pseudo-Reference Genome (PRG) assembly file.
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Title sample_1_to_12_mpileup
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Description This is the pileup file (see VarScan application).
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Title Supplementary Tables
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Description Supplementary tables
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Title Fig_S1
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Description FIGURE S1. Fraction of missing SNP calls in each individual.
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Title Fig_S2
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Description FIGURE S2. Number of 100-bp Illumina reads per individual. Individual labels refer to those used in Table S4 and Figure 5.
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Title Fig_S3
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Description FIGURE S3. STRUCTURE plots showing 10 in-group individuals for three replicated runs (‘rep’) using all available SNPs polymorphic in the ingroup lineages that mapped to the zebra finch genome (n = 9525) with K = 2 (upper panel) and K = 3 (lower panel).
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Title Fig_S4
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Description FIGURE S4. STRUCTURE plots showing 10 in-group individuals for three replicated runs (‘rep’) in which we excluded SNPs whose coverage amongst called individuals was greater than two standard deviations above the mean (n = 32,103) with K = 2 (upper panel) and K = 3 (lower panel).
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Title Fig_S5
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Description FIGURE S5. Parsimony consensus tree (outgroups not shown) using a stepmatrix in which each genotype is one step from the adjacent one sharing one allele, with heterozygotes being one step from each homozygote but the two homozygotes being two steps from each other; bootstrap support numbers at nodes are based on 2000 replicates; only bootstrap >50 is shown.
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Title Fig_S6
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Description FIGURE S6. (a) Number of contigs mapped against zebra finch chromosomes plotted versus chromosome length; fewer contigs mapped against the Z chromosome (blue) than expected by chromosome length. (b) Number of contigs that contain a SNP with an ABBA or BABA pattern mapped against zebra finch chromosomes versus chromosome length; far fewer ABBA-BABA contigs mapped against the Z chromosome (blue) than expected by chromosome length. (c) Number of contigs that contain an ABBA or BABA pattern versus number of total contigs for each zebra finch chromosome they mapped against; fewer ABBA-BABA contigs mapped to the Z chromosome (blue) than expected. (d) Frequency plot giving the number of ABBA-BABA contigs mapped against each zebra finch chromosome per contigs mapped.
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Title Fig_S7
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Description FIGURE S7. Illustration of an example case of ancient population subdivision that could lead to an identical data signal as that created by genetic introgression between mosaic birds and Z. chrysops. Note that substantial levels of persistent ancestral subdivision (across speciation events) are needed to account for such patterns of asymmetry of tree signal (Slatkin and Pollard 2008). Given most Andean birds’ turbulent Pleistocene evolutionary history, this alternative scenario is probably unlikely.
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When using this data, please cite the original publication:

Rheindt FE, Fujita MK, Wilton PR, Edwards SV (2013) ntrogression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): population genetic and phylogenetic inferences from genome-wide SNPs. Systematic Biology 63(2): 134-152. http://dx.doi.org/10.1093/sysbio/syt070

Additionally, please cite the Dryad data package:

Rheindt FE, Fujita MK, Wilton PR, Edwards SV (2013) Data from: Introgression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): population genetic and phylogenetic inferences from genome-wide SNPs. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.633bk
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