Data from: You are where you live: parasitic nematode mitochondrial genome size is associated with the thermal environment generated by hosts

Lagisz M, Poulin R, Nakagawa S

Date Published: November 13, 2012

DOI: http://dx.doi.org/10.5061/dryad.kf490

 

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Title Lagisz_DATATABLE
Description General description : the table contains genetic and phenotypic data for 47 Nematoda species and 2 outgroup species. Table columns: ord - numerical ordering of the table in order of data collection. animal - specie's full latin name. Refseq - specie's Refseq code. NCBItaxID - specie's taxonomic ID from NCBI. genus - specie's genus name. species - species name. host - main definitive host or habitat. host_code - main definitive host code: 0 = free-living or plant-parasitic, 1 = parasite of endotherms, -1 = parasite of ectotherms. class - specie's taxonomic class. reproduction - specie's reprodactive mode: dioecy, hermaphroditism, androdioecy. max_male_length - maximum length of males [mm]. av_male_width - average male width [mm]. av_female_length - average female length [mm]. max_female_width - maximum female width [mm]. size_sources - literature sources for body size measurements. volume_male - calculated male body volume [mm3]. volume_female - calculated female body volume [mm3]. log_volume_male- logarithm of male body volume. log_volume_female- logarithm of female body volume. genome_length - species mitogenome sequence length [bp]. p_GC_content - percent of GC base content of the mitogenomic sequence. p_prot_coding - percent of protein-coding bases in the mitogenomic sequence. p_coding - percent coding bases in the mitogenomic sequence. N_cDNAs - number of protein-coding genes in the mitogenome. N_tRNAs - number of tRNA-coding genes in the mitogenome. N_rRNAs - number of rRNA-coding genes in the mitogenome. bp_cDNAs - length of protein-coding sequence in the mitogenome [bp]. bp_tRNAs - length of tRNA-coding sequence in the mitogenome [bp]. bp_rRNAs - length of rRNA-coding sequence in the mitogenome [bp]. bp_noncoding - length of non-coding sequence in the mitogenome [bp]. N_repeats - number of repeats in the mitogenome. bp_repeats - length of repeat sequence in the mitogenome [bp]. p_repeats - percent of repeat sequence in the mitogenome. go_dist_anc - rearrangement distance from the estimated most recent ancestror of Nematoda, estimated with MGR software. subs_rate - species amino-acid substitution rate in the mitogenome, estimated with BEAST.
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Title Lagisz_tree_PHYML
Description Maximum Likelihood phylogenetic tree of 47 Nematoda species and 2 outgroup species created with PHYML software and based on concatenated aa sequences of mitochondrial protein-coding genes.
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Title Lagisz_tree_BEAST
Description Bayesian phylogenetic tree of 47 Nematoda species and 2 outgroup species created with BEAST software and based on concatenated aa sequences of mitochondrial protein-coding genes.
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Title Lagisz_tree_NCBI
Description Ultrametric topological phylogenetic tree of 47 Nematoda species created from NCBI taxonomy with polytomies resolved at random.
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Title Lagisz_gene_orders_coded_MGR
Description Protein-coding gene orders of 47 Nematoda species and 2 outgroup species coded for analyses with MGR software. Codes: 1 = ATP6, 2 = COX1, 3 = COX2, 4 = COX3, 5 = CYTB, 6 = ND1, 7 = ND2, 8 = ND3, 9 = ND4, 10 = ND4L, 11 = ND5, 12 = ND6
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Title Lagisz_aa_alignment_BLOCKS
Description Amino acid sequence alignment of the protein-coding genes from mitogenomes of 47 Nematoda species and 2 outgroup species. The sequences were aligned individually for each gena and de-gapped using BLOCKS program and then concatenated into a single alignment for analyses.
Download Lagisz_aa_alignment_BLOCKS.fas (158.5 Kb)
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When using this data, please cite the original publication:

Lagisz M, Poulin R, Nakagawa S (2013) You are where you live: parasitic nematode mitochondrial genome size is associated with the thermal environment generated by hosts. Journal of Evolutionary Biology 26(3): 683-690. http://dx.doi.org/10.1111/jeb.12068

Additionally, please cite the Dryad data package:

Lagisz M, Poulin R, Nakagawa S (2013) Data from: You are where you live: parasitic nematode mitochondrial genome size is associated with the thermal environment generated by hosts. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.kf490
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