DOI: 10.5061/dryad.4f4qrfjqf
title: Mitochondrial genes have incongruent histories linked to their chromosomal position and function

description: Mitochondrial DNA has been one of the key workhorses of evolutionary
 studies. Hence understanding the dynamics of DNA sequence change in this
 tiny genome (15 to 20 kilobases) is of utmost importance. However, we are
 unaware of large studies examining how the functionality and chromosomal
 positioning of mitochondrial genes may impact the evolutionary histories
 that they depict. To examine this, we assembled a large database of animal
 mitochondrial genomes (&gt; 10,000 total individuals over 89 taxonomic
 groups) and compared their phylogenetics, functionality, and location on
 the mitochondrial genome (heavy or light strand, and distance from origin
 of replication). We found that many genes show unique evolutionary
 patterns, often directly tied to chromosomal location or function of the
 gene (e.g. NADH dehydrogenases or ribosomal genes). We also found rampant
 phylogenetic incongruence among the linked genes of the mitochondrial
 circular chromosome in most of the taxonomic groups we examined. These
 results suggest mitochondrial genomes have accrued complex evolutionary
 patterns. The accumulated incongruence can influence phylogenetic
 inference in evolutionary studies, making mito-gene choice for
 phylogenetics critical. The phenomena we show here should also be examined
 in other organelle and even nuclear gene studies.
description: # Mitochondrial genes have incongruent histories linked to their
 chromosomal position and function Dataset DOI:
 [10.5061/dryad.4f4qrfjqf](10.5061/dryad.4f4qrfjqf) **Description of the
 data and file structure** This site holds the data used for a study by
 DeSalle and Tessler entitled "Mitochondrial genes have incongruent
 phylogenetic patterns linked to their chromosomal position and
 function". 1.     The file entitled "Mitom_Supplemental
 XXXXXXXXTable 1.xlsx" is an Excel file with tabbed sheets. The first
 sheet holds all of the accession numbers of the genomes used in the study.
 The second sheet holds a table showing the phylogenetic distribution of
 the animal groups examined in the study. The third sheet gives the names
 of the nexus files for each taxon included in the study. The column
 headers in the table 1 tab are defined as follows *Abbrev*: Abbreviation
 used in study. *scientific name*: Full binomial names of the taxa in the
 study           *common name*: The taxonomic groups common names like
 “fish”, “mammal” “insect” or “birtf” *Taxonomic ID*:  Genbank taxonomic ID
 number *Rank*: We attempted to focus on ordinal (order) level matrices,
 but occasional we had to use a different taxonomic level.  Levels used
 are: order, superorder, infraorder, subphyla, subclass, no rank (clade)
 and phylum. *Ntaxa*: the number of taxa in the matrices.               
 For Supplemental Table 1, the header of the columns holds the primary
 scientific name of the group used. 2.     The file named
 "mitomania1_Supplemental_File_2 copy.xlsx" gives the raw
 incongruence data used to construct the heat maps in the paper. The
 "READ ME" TAB in this file explains how to use the spreadsheet.
 Specifically, a.     The data recorded are 0's (incongruent) and
 1's (congruent) b.     Raw test scores are given in the sheet with
 the taxon name or common name. c.     Raw scores with heat map stripped
 away are given in sheets labeled with a "7" d.     The tabs in
 this spreadsheet are: insect7, mollusc7, crustacea7, othr inv7, birds7,
 mammals7, fish7, other verts7, echino7, and Diploblasts7. And include the
 raw incongruence scores for all comparisons in the indicated taxonomic
 group (ie. fish, bird, etc.) 3.     The third file named
 "Mito_partitioned_nexus_files.zip" is a compressed zip file with
 the 89 nexus matrices, fully partitioned and labeled by taxon that were
 used in the incongruence measures. Follows is a table with the file names
 and taxon designations: | **Taxonomic Group** | Concatenated file | |
 :--------------------- | :------------------------- | | **Achelata** |
 achelata.cat.cat.cat | | **Acipenseridae** | acipenser.cat.cat.cat | |
 **Aedes** | aedes.cat.cat.cat | | **Afrotheria** | Afroth.cat.cat.cat | |
 **Alepocephaliformes** | alepo.cat.cat.cat | | **Anguilliformes** |
 anguliformes.cat.cat.cat | | **Annelida** | annelida.cat.cat.cat | |
 **Anomura** | anomura.cat.cat.cat | | **Anopheles** | anoph.cat.cat.cat |
 | **Anura** | anura.cat.cat.cat | | **Arachnida** | arachnida.cat.cat.cat
 | | **Aschiza** | Asciz.cat.cat.cat | | **Asterozoa** | astro.cat.cat.cat
 | | **Atlantogenata** | Atlanto.cat.cat.cat | | **Bibniomorpha** |
 Bibnio.cat.cat.cat | | **Blattodea** | Blatt.cat.cat.cat | | **Bovidae** |
 bovidae.cat.cat.cat | | **Brachyura** | Brachyura.cat.cat.cat | |
 **Branchiostoma** | branchio.cat.cat.cat | | **Bucerotiformes** |
 bucer.cat.cat.cat | | **Caenogastropoda** | Caenogastr.cat.cat.cat | |
 **Carcharhiniformes** | carchar.cat.cat.cat | | **Carnivora** |
 carnivora.cat.cat.cat | | **Cephalopoda** | cephalopoda.cat.cat.cat | |
 **Cetacea** | cetacea.cat.cat.cat | | **Charadriiformes** |
 charad.cat.cat.cat | | **Chimaeriformes** | chimaer.cat.cat.cat | |
 **Chiroptera** | Chiroptera.cat.cat.cat | | **Chondrichthyes** |
 chondry.cat.cat.cat | | **Characiformes** | chrac.cat.cat.cat | |
 **Chromadorea** | chroma.cat.cat.cat | | **Clupeiformes** |
 clup.cat.cat.cat | | **Cnidaria** | cnidaria.cat.cat.cat | |
 **Coleoptera** | coleoptera.cat.cat.cat | | **Columbiformes** |
 columb.cat.cat.cat | | **Copepoda** | copep.cat.cat.cat | |
 **Coraciformes** | corac.cat.cat.cat | | **Crocodylia** | croc.cat.cat.cat
 | | **Ctenophora** | cteno.cat.cat.cat | | **Culex** | culex.cat.cat.cat |
 | **Cyprinidae** | cyprionid.cat.cat.cat | | **Dendrobranchiata** |
 dendro.cat.cat.cat | | **Eleutheria** | eleuth.cat.cat.cat | | **Enoplea**
 | enop.cat.cat.cat | | **Falconiformes** | falcon.cat.cat.cat | |
 **Hemiptera** | hemiptera.cat.cat.cat | | **Heterobranchia** |
 heterobranchia.cat.cat.cat | | **Hoplocarida** | Hoplo.cat.cat.cat | |
 **Hymenoptera** | hymenoptera.cat.cat.cat | | **Eulipotyhyla** |
 insectivore.cat.cat.cat | | **Termitoidae** | isoptera.cat.cat.cat | |
 **Lagomorpba** | lago.cat.cat.cat | | **Lamniformes** | lamni.cat.cat.cat
 | | **Lepidoptera** | lepidoptera.cat.cat.cat | | **Mantodea** |
 mantod.cat.cat.cat | | **Metatheria** | marsupial.cat.cat.cat | |
 **Mecoptera** | mecop.cat.cat.cat | | **Megaloptera** | megal.cat.cat.cat
 | | **Myliobatiformes** | mylio.cat.cat.cat | | **Myriapoda** |
 myria.cat.cat.cat | | **Nemertia** | nemer.cat.cat.cat | |
 **Neritimorpha** | nerit.cat.cat.cat | | **Odonata** | odon.cat.cat.cat |
 | **Osteoglossiformes** | osteog.cat.cat.cat | | **Palaeognatha** |
 Paleog.cat.cat.cat | | **Palaeoheterdonta** | paleohet.cat.cat.cat | |
 **Pelmatozoa** | pelmeto.cat.cat.cat | | **Perciformes** |
 peric.cat.cat.cat | | **Phasmatodea** | Phasm.cat.cat.cat | |
 **Piciformes** | picif.cat.cat.cat | | **Plecoptera** |
 Plecoptera.cat.cat.cat | | **Porifera** | porifera.cat.cat.cat | |
 **Prlmates** | primate.cat.cat.cat | | **Psittaciformes** |
 Psitta.cat.cat.cat | | **Psocodea** | Psoco.cat.cat.cat | |
 **Pteriomorpa** | pteriomorpha.cat.cat.cat | | **Placozoa** |
 pzoa.cat.cat.cat | | **Rhinopristiformes** | rhino.cat.cat.cat | |
 **Rodentla** | rodent.cat.cat.cat | | **Salmoniformes** |
 salmo.cat.cat.cat | | **Serpentes** | serpent.cat.cat.cat | |
 **Siphonaptera** | Siph.cat.cat.cat | | **Squaliformes** |
 Squal.cat.cat.cat | | **Strigiformes** | strig.cat.cat.cat | |
 **Testudines** | test.cat.cat.cat | | **Zygentoma** | Thys.cat.cat.cat | |
 **Trlchoptera** | trichop.cat.cat.cat | | **Vetigastropoda** |
 vetig.cat.cat.cat | | **Xenarthra** | xen.cat.cat.cat | 4.     The fourth
 file – “Mitomania_Supplemental_File2.docx" holds the analysis of
 alignment aware versus alignment agnostic incongruences. ## Access
 information Other publicly accessible locations of the data: The
 individual sequences used for this study are from GenBank and the
 accession numbers are given in these files. Data was derived from the
 following sources: NIH NCBI GenBank