Mitochondrial genes have incongruent histories linked to their chromosomal position and function
Data files
Apr 16, 2025 version files 63.99 MB
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Mito_partitioned_nexus_files.zip
62.73 MB
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Mitom_Supplemental_XXXXXXXXTable_1.xlsx
203.16 KB
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Mitomania_Supplemental_File2.docx
537.28 KB
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mitomania1_Supplemental_File_3_copy.xlsx
511.01 KB
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README.md
8.06 KB
Abstract
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 (> 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.
Dataset DOI: 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