Data from: Incorporating color into integrative taxonomy: analysis of the varied tit (Sittiparus varius) complex in East Asia

McKay BD, Mays Jr. HL, Yao C, Wan D, Higuchi H, Nishiumi I

Date Published: February 28, 2014

DOI: http://dx.doi.org/10.5061/dryad.6q44t

 

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Title ND2 locus alignment
Downloaded 13 times
Description ND2 locus alignment in fasta format
Download VATI ND2 Align Final.fasta (90.44 Kb)
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Title 08352 locus alignment
Downloaded 14 times
Description 08352 locus phased alignment in fasta format
Download VATI CS08352 Align Final.fas (19.15 Kb)
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Title 09385 locus alignment
Downloaded 8 times
Description 09385 locus phased alignment in fasta format
Download VATI CS09385 Align Final.fas (15.87 Kb)
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Title 10179 locus alignment
Downloaded 12 times
Description 10179 locus phased alignment in fasta format
Download VATI CS10179 Align Final.fas (31.78 Kb)
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Title 11887 locus alignment
Downloaded 13 times
Description 11887 locus phased alignment in fasta format
Download VATI CS11887 Align Final.fas (9.506 Kb)
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Title 12884 locus alignment
Downloaded 11 times
Description 12884 locus phased alignment in fasta format
Download VATI CS12884B Align Final.fas (18.86 Kb)
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Title 15349 locus alignment
Downloaded 13 times
Description 15349 locus phased alignment in fasta format
Download VATI CS15349 Align Final.fas (18.61 Kb)
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Title Table S1. Morphological sample list
Downloaded 44 times
Description Museum voucher information for all skin specimens of the varied tit (Sittiparus varius) complex examined in this study. Tissue voucher numbers are provided for the few cases in which an individual was sampled for both morphological and genetic data. Acronyms: National Museum of Nature and Science, Tokyo (NSMT); American Museum of Natural History (AMNH); Yamashina Institute of Ornithology (YIO); National Museum of Natural Science, Taiwan (NMNS), Taiwan Endemic Species Research Institute (TESRI).
Download S1 Morphological sample list.pdf (66.94 Kb)
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Title Table S2. Molecular sample list
Downloaded 29 times
Description Museum voucher information for all genetic samples of the varied tit (Sittiparus varius) complex used in this study. Stars indicate individuals selected for multilocus nuclear sequencing. Acronyms: National Museum of Nature and Science, Tokyo (NSMT); Taiwan Endemic Species Research Institute (TESRI); Liaoning University, China (LU); Cincinnati Museum Center (CMC); American Museum of Natural History (AMNH); University of Kansas University Natural History Museum (KUNMH).
Download S2 Molecular sample list.pdf (69.28 Kb)
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Title Table S3. Toepad primers & sequencing conditions
Downloaded 246 times
Description A list of primers used to amplify and sequence the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene from a toepad sample of Sittiparus varius orii. Detailed DNA extraction, PCR, and sequencing protocols for toepad samples are also given.
Download S3 Toepad primers & sequencing conditions.pdf (81.67 Kb)
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Title Figure S4. Morphometric plots
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Description Boxplots of morphometric size variation among subspecies of the varied tit (Sittiparus varius) complex: (a) bill length, (b) bill depth, (c) bill width, (d) tarsus length, (e) wing chord, and (f) tail length. The taxon castaneoventris showed non-overlapping size variation in bill depth, wing chord, and tail length. Heavy lines inside boxes represent the mediums (second quartiles). Each box is bounded by the first and third quartiles, and plot whiskers extend to 1.5 times the interquartile range or to the maximum and minimum value, as appropriate. Data points outside the whisker range are represented by open circles.
Download S4 Morphometric plots.pdf (313.9 Kb)
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Title Figure S5. Luminance plots
Downloaded 48 times
Description Boxplots of luminance measurements obtained from plumage patches with <0.05 luminance reflectance: (a) mantle, (b) throat, and (c) black of head. Hue measurements were excluded from these patches because very dark colors yield random hues when converted into opponent colorspace. Each box is bounded by the first and third quartiles, and plot whiskers extend to 1.5 times the interquartile range or to the maximum and minimum value, as appropriate. Data points outside the whisker range are represented by open circles.
Download S5 Luminance plots.pdf (279.1 Kb)
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Title Table S6. Loci table
Downloaded 28 times
Description Descriptive statistics for the seven molecular loci used to construct phylogenetic relationships among S. varius, S. castaneoventris, S. owstoni, and S. olivaceus. The summary includes the length of the sequences (in base pairs), the number of alleles, the number of segregating sites (s), the number of parsimony-informative sites (PI sites), nucleotide diversity (π), and the nucleotide substitution model. Statistics are drawn from ingroup sequences only. Note that ND2 statistics are drawn from a reduced ND2 alignment, which comprised the 16 samples sequenced for nuclear loci.
Download S6 Loci table.pdf (62.54 Kb)
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Title Figure S7. Nuclear intron networks
Downloaded 42 times
Description Statistical parsimony networks of nuclear intron sequences: (a) 08352, (b) 09385, (c) 10179, (d) 11887, (e) 12884, and (f) 15349. Each circle represents a haplotype; the size of the circle is proportional to a haplotype’s frequency. Small black circles represent inferred haplotypes. Colors distinguish the four species recognized in this study.
Download S7 Nuclear intron networks.pdf (204.9 Kb)
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When using this data, please cite the original publication:

McKay BD, Mays Jr HL, Yao C, Wan D, Higuchi H, Nishiumi I (2014) Incorporating color into integrative taxonomy: analysis of the varied tit (Sittiparus varius) complex in East Asia. Systematic Biology 63(4): 505-517. http://dx.doi.org/10.1093/sysbio/syu016

Additionally, please cite the Dryad data package:

McKay BD, Mays Jr. HL, Yao C, Wan D, Higuchi H, Nishiumi I (2014) Data from: Incorporating color into integrative taxonomy: analysis of the varied tit (Sittiparus varius) complex in East Asia. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6q44t
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