Data from: Phylogenetic signal variation in the genomes of Medicago (Fabaceae)

 

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Title chloroplast
Downloaded 65 times
Description Concatenated alignment of single-nucleotide variants from the chloroplast in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
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Title chromosome 1
Downloaded 57 times
Description Concatenated alignment of single-nucleotide variants from chromosome 1 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
Download chr1_29_ab.phy (298.7 Kb)
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Title chromosome 2
Downloaded 39 times
Description Concatenated alignment of single-nucleotide variants from chromosome 2 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
Download chr2_29_ab.phy (300.1 Kb)
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Title chromosome 3
Downloaded 36 times
Description Concatenated alignment of single-nucleotide variants from chromosome 3 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
Download chr3_29_ab.phy (390.7 Kb)
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Title chromosome 4
Downloaded 44 times
Description Concatenated alignment of single-nucleotide variants from chromosome 4 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
Download chr4_29_ab.phy (385.8 Kb)
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Title chromosome 5
Downloaded 37 times
Description Concatenated alignment of single-nucleotide variants from chromosome 5 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
Download chr5_29_ab.phy (448.8 Kb)
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Title chromosome 6
Downloaded 38 times
Description Concatenated alignment of single-nucleotide variants from chromosome 6 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
Download chr6_29_ab.phy (78.77 Kb)
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Title chromosome 7
Downloaded 43 times
Description Concatenated alignment of single-nucleotide variants from chromosome 7 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
Download chr7_29_ab.phy (360.5 Kb)
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Title chromosome 8
Downloaded 36 times
Description Concatenated alignment of single-nucleotide variants from chromosome 8 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
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Title Figure S01
Downloaded 73 times
Description The posterior consensus topology estimated from the concatenated nuclear genomic dataset in our Bayesian analysis (left) compared to a maximum parsimony topology estimated from the same data set (right). On both trees, support for nodes (posterior support for the Bayesian consensus, bootstrap support from 500 replicates for the MP tree) is indicated: black filled circles, ≥ 0.95; gray, between 0.95 and 0.75; white, < 0.75. On the right-hand tree, arrows indicate nodes in conflict with the Bayesian consensus. Scale bar indicates branch length in expected substitutions per site.
Download figS01-MB-PA_comp.pdf (7.51 Kb)
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Title Figure S02
Downloaded 69 times
Description Phylogenetic estimates from sites on each of the chromosomes and the chloroplast. Each tree is the Bayesian consensus tree estimated for the concatenated variable sites on each chromosome and the chloroplast, with posterior support indicated at each node: black filled circles, ≥ 0.95; gray, between 0.95 and 0.75; white, < 0.75. Scale bars indicate branch length in expected substitutions per site.
Download figS02-chromtrees_MBcon_r02.pdf (16.03 Kb)
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Title Figure S03
Downloaded 97 times
Description Genomic location of sliding windows with strong (≥ 0.95) posterior support for the four topological rearrangements most commonly given strong support by individual sliding windows. Filled circles indicate the weighted conflict score for the consensus tree estimated from a given sliding window of 500 consecutive sites; red circles indicate windows whose consensus topology strongly supports the given rearrangement.
Download figS03-recurrent_conflict4_r04.pdf (108.0 Kb)
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When using this data, please cite the original publication:

Yoder JB, Briskine R, Mudge J, Farmer A, Paape T, Steele K, Weiblen GD, Bharti AK, Zhou P, May GD, Young ND, Tiffin P (2013) Phylogenetic signal variation in the genomes of Medicago (Fabaceae). Systematic Biology 62(3): 424-438. http://dx.doi.org/10.1093/sysbio/syt009

Additionally, please cite the Dryad data package:

Yoder JB, Briskine R, Mudge J, Farmer A, Paape T, Steele K, Weiblen GD, Bharti AK, Zhou P, May GD, Young ND, Tiffin P (2013) Data from: Phylogenetic signal variation in the genomes of Medicago (Fabaceae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.vp634306
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