DOI: 10.5061/dryad.kf490
title: Data from: You are where you live: parasitic nematode mitochondrial genome size is associated with the thermal environment generated by hosts

description: There exists remarkable interspecific variation in mitochondrial sequence
 evolution rates and in mitochondrial genome sizes. A number of hypotheses
 based on the forces of mutation and selection have been proposed to
 explain this variation. Among such hypotheses, we test three: 1) the
 ‘longevity-dependent selection’, 2) the ‘functional constraints’ and 3)
 the ‘race for replication’ hypotheses, using published mtDNA genomic
 sequences of 47 Nematoda species. We did not find any relationship between
 body size (used as a proxy for longevity) and genome size or the
 substitution rate of protein sequences, providing little evidence for the
 first hypothesis. Parasitic species from different thermal habitats, as
 determined by their definitive host type (ectothermal vs. endothermal),
 did not differ in their rates of protein evolution. Therefore, little
 support was obtained for the second hypothesis. However, we revealed that
 mitogenomes of parasites of endotherms were significantly smaller than
 those of parasites of ectotherms, supporting the race for replication
 hypothesis. As mitochondrial genomes of endothermal animals are usually
 more compact than those of ectothermal animals, intriguingly, nematode
 parasites of endotherms and ectotherms exhibit similar patterns of mtDNA
 length variation to their hosts.
description: Lagisz_DATATABLEGeneral 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.Lagisz_tree_PHYMLMaximum 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.Lagisz_tree_BEASTBayesian 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.Lagisz_tree_NCBIUltrametric topological phylogenetic tree of 47 Nematoda species created from NCBI taxonomy with polytomies resolved at random.Lagisz_gene_orders_coded_MGRProtein-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 = ND6Lagisz_aa_alignment_BLOCKSAmino 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.