16 research outputs found

    Additional file 4: Table S2. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

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    v2. Cytochrome b blast validation. Best hits to GenBank entries for cytochrome b genes from assembled mitochondrial genomes. For N. mexicana, the best hit was to a closely related species, with the second best hit to N. mexicana. (XLS 38 kb

    Additional file 2: of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

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    Whole mitochondrial exomes. Description: Alignment of the protein coding genes of each assembled mitogenome along with Akodon montensis, downloaded from GenBank. (TXT 257 kb

    Additional file 3: Figure S1. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

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    Cytochrome b phylogenetic validation. ML tree of the assembled cytochrome b sequences compared with cytochrome b sequences downloaded from GenBank. These results showed if the sequences from our data correlated with known cytb sequences. (PNG 60 kb

    Additional file 1: Table S1. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

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    Title of data: Cytochrome b GenBank information. Taxa names and accession numbers for cytochrome b genes downloaded from GenBank in Additional file 3: Figure S1. (XLS 28 kb

    assembled_contigs_from_UCEenriched_reads

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    All loci assembled from baited reads (per taxa). These sequences were then compared in an all-vs-all manner to identify homologous UCE loci among taxa. As a results, there are some contigs that may not be present in the final alignments since they are not UCE loci

    Individual gene trees from UCE loci

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    Individual gene trees per UCE locus were generated using RAxML's GTRGAMMA model of nucleotide evolution and fast bootstrapping options (replicates=1,000). Individual trees are in Newick format
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