DOI: 10.5061/dryad.tx95x6b9w
title: Accelerated mitochondrial genome evolution in parasitic barnacles driven by adaptive and non-adaptive responses

description: Parasitic lifestyles often impose profound evolutionary pressures,
 affecting molecular evolution through both adaptive and non-adaptive
 mechanisms. Among barnacles (subclass Cirripedia), the obligate parasitic
 Rhizocephala differ markedly from their filter-feeding thoracican
 relatives in morphology, ecology, and life history. However, how the shift
 to parasitism has shaped mitochondrial genome evolution within Cirripedia
 remains unclear. Here, we present the first comprehensive comparative
 analysis of mitochondrial genomes between parasitic and non-parasitic
 barnacles, including three newly sequenced and one previously unpublished
 species of parasitic Rhizocephala, a clade whose mitochondrial genomes had
 not been characterized until now. Phylogenomic and molecular evolutionary
 analyses reveal that Rhizocephala species exhibit extremely long branches,
 likely attributed to the clade-specific tempo (high substitution rate) and
 mode (selection pressure) of mtDNA sequence evolution associated with
 their parasitic lifestyle. A two-cluster molecular clock test reveals
 significantly elevated substitution rates across rhizocephalans,
 consistent with reduced effective population sizes (Ne) linked to their
 opportunistic, host-dependent life cycles. We also detect signatures of
 positive selection in protein-coding genes encoding key components of the
 electron transport chain complexes III and IV. Structural modeling
 highlights amino acid substitutions at functionally critical sites for
 electron transfer and proton pumping, suggesting adaptive modifications to
 mitochondrial bioenergetics under hypoxic conditions within host tissues.
 Together, our findings underscore that both non-adaptive (genetic drift,
 relaxed selection) and adaptive (positive selection) processes have driven
 the rapid sequence divergence of mitochondrial genomes in parasitic
 Rhizocephala. Further experimental study is needed to elucidate how
 mitochondrial and nuclear-encoded subunits of oxidative phosphorylation
 coevolve in this specialized parasitic group.
description: # Accelerated mitochondrial genome evolution in parasitic barnacles driven
 by adaptive and non-adaptive responses Dataset DOI:
 [10.5061/dryad.tx95x6b9w](https://doi.org/10.5061/dryad.tx95x6b9w) ##
 Description of the data and file structure Data and script files used for
 the analyses in the manuscript "Accelerated Mitochondrial Genome
 Evolution in Parasitic Barnacles Driven by Adaptive and Non-Adaptive
 Responses." ### Files and variables #### File: 18S_Gblocks.fas
 **Description:** Input file containing aligned 18S rDNA sequences used for
 phylogenetic reconstruction #### File: 18S_Gblocks.nj
 **Description:** Input neighbor-joining (NJ) tree file for the two-cluster
 test using 18S rDNA sequences in LINTRE #### File: 18S_Gblocks.phy
 **Description:** Input sequence file for the two-cluster test using 18S
 rDNA sequences in LINTRE #### File: atp6.fasta **Description:** Input
 sequence files for each of the 13 mitochondrial protein-coding genes
 (PCGs) and their concatenated alignment used in HyPhy analysis #### File:
 atp8.fasta **Description:** Input sequence files for each of the 13
 mitochondrial protein-coding genes (PCGs) and their concatenated alignment
 used in HyPhy analysis #### File: cirripedia_hyphy.tree
 **Description:** Input tree file with background and foreground branches
 labeled for HyPhy analysis #### File: cirripedia_concatenated.fasta
 **Description:** Input sequence files for each of the 13 mitochondrial
 protein-coding genes (PCGs) and their concatenated alignment used in HyPhy
 analysis #### File: cirripedia_mt_cds.nj **Description:** Input
 neighbor-joining (NJ) tree file for the two-cluster test using mtDNA
 sequences in LINTRE #### File: cirripedia_tree.nwk
 **Description:** Phylogenetic tree file (Newick format) used as input for
 codon-based selection analyses in PAML #### File: cirripedia_mt_cds.nuc
 **Description:** Input sequence file for the two-cluster test using mtDNA
 sequences in LINTRE #### File: cob.fasta **Description:** Input sequence
 files for each of the 13 mitochondrial protein-coding genes (PCGs) and
 their concatenated alignment used in HyPhy analysis #### File: cox2.fasta
 **Description:** Input sequence files for each of the 13 mitochondrial
 protein-coding genes (PCGs) and their concatenated alignment used in HyPhy
 analysis #### File: cox3.fasta **Description:** Input sequence files for
 each of the 13 mitochondrial protein-coding genes (PCGs) and their
 concatenated alignment used in HyPhy analysis #### File: nad1.fasta
 **Description:** Input sequence files for each of the 13 mitochondrial
 protein-coding genes (PCGs) and their concatenated alignment used in HyPhy
 analysis #### File: run_BUSTED.sh **Description:** Batch run script for
 BUSTED analysis #### File: codeml_mt_cds.ctl **Description:** Input
 control file used in PAML analysis #### File: cox1.fasta
 **Description:** Input sequence files for each of the 13 mitochondrial
 protein-coding genes (PCGs) and their concatenated alignment used in HyPhy
 analysis #### File: nad4L.fasta **Description:** Input sequence files for
 each of the 13 mitochondrial protein-coding genes (PCGs) and their
 concatenated alignment used in HyPhy analysis #### File: nad4.fasta
 **Description:** Input sequence files for each of the 13 mitochondrial
 protein-coding genes (PCGs) and their concatenated alignment used in HyPhy
 analysis #### File: nad6.fasta **Description:** Input sequence files for
 each of the 13 mitochondrial protein-coding genes (PCGs) and their
 concatenated alignment used in HyPhy analysis #### File: nad5.fasta
 **Description:** Input sequence files for each of the 13 mitochondrial
 protein-coding genes (PCGs) and their concatenated alignment used in HyPhy
 analysis #### File: run_RELAX.sh **Description:** Batch run script for
 RELAX analysis #### File: gene_order_crex_2.txt **Description:** Input
 data file for phylogenetic analysis based on mitochondrial gene order
 information #### File: nad3.fasta **Description:** Input sequence files
 for each of the 13 mitochondrial protein-coding genes (PCGs) and their
 concatenated alignment used in HyPhy analysis #### File: nad2.fasta
 **Description:** Input sequence files for each of the 13 mitochondrial
 protein-coding genes (PCGs) and their concatenated alignment used in HyPhy
 analysis #### File: cirripedia_mtDNA_alignment_without_3rd_codons.fasta
 **Description:** Concatenated nucleotide sequences of 13 mitochondrial
 protein-coding genes with third codon positions excluded. This dataset was
 used as input for phylogenetic tree inference #### File:
 cirripedia_mtDNA_sequence_alignment_with_3rd_codons.fasta
 **Description:** Concatenated nucleotide sequences of 13 mitochondrial
 protein-coding genes with third codon positions included #### File:
 cirripedia_mt_cds_volcano.phy.txt **Description:** Input file containing
 concatenated mitochondrial codon sequences used for PAML analysis