6. Adding order and family classification schemes from Fishes of the World (5th edition)

• We use R to add in the order and family numbers from the classifications scheme used in "Fishes of the World, 5th edition" (Nelson et al. 2016) , a widely used reference book in fish systematics.

• In this scheme, fish orders are numbered from 1 to 85, while families are numbered from 1 to 536.

• Data files for the classification scheme are available in the db.scripts/FotW5_classification folder in the mitohelper repository:

1. • A detailed version of the classification scheme (FotW5Classification.pdf)
2. • Tab-separated text file of the order classification scheme (FotW5_order.tsv)
3. • Tab-separated text file of the family classification scheme (FotW5_family.tsv)

R commands to merge reference tables with Fishes of the World classification

# Import relevant files
mitofish=read.delim("mitofish.ref.tsv",header=T,sep="\t")
order=read.delim("FotW5_order.tsv",header=T,sep="\t")
family=read.delim("FotW5_family.tsv",header=T,sep="\t")

# Merge tables
ordermerge=merge(mitofish,order,by="Order",all.x=TRUE)
familymerge=merge(ordermerge,family,by="Family",all.x=TRUE)

# Output new table
write.table(familymerge,"mitofish.ref2.tsv",sep="\t")

Reformat output table

cat mitofish.ref2.tsv | tr -d "\"" | sed "s/^Family/#Family/" | tr "#" "\t" | awk -F "\t" '{OFS="\t"}{print $4,$5,$6,$7,$8,$9,$3,$2,$10,$11,$12,$13,$14}' | sed "s/Gene.definition/Gene definition/" >mitofish.final.tsv

Final merged table

• The column OrderID contains order numbers assigned by "Fishes of the World, 5th edition" (Nelson et al. 2016)
• The column FamilyID contains family numbers assigned by "Fishes of the World, 5th edition" (Nelson et al. 2016)
• "Fishes of the World, 5th edition" (Nelson et al. 2016) was last updated in 2018 and is outdated.
• Therefore, some of the new or re-classified fish orders and families are not yet classified in the book.
• These have NA values in the OrderID or FamilyID columns.

Accession       Gene definition taxid   Superkingdom    Phylum  Class   Family  Order   Genus   Species Sequence        OrderID FamilyID
U46868  Macquaria novemaculeata mitochondrial DNA control region haplotype      45783   Eukaryota       Chordata        Actinopteri     'Percalatidae'  Centrarchiformes        Percalates      Percalates novemaculeata        ACACCATACATTTATATTAACCATATCAGGGGTATTCAAGGACATATATGTTTTATCAACATTTCTCGTATTACACCATTCATATATCACTTAAACAAGAAGAATTCCATAACCCATTAAAAGTATACCGTATATAAATGAAATCTGGGATGGGCGAAATTTAAGACCGAGCACAATCACTCATAAGGTTAAGATATACCAGGACTCAACATATAGACATTCTTCACAATCTTAATGTAGTAAGAACCGACCAACAGTGATTTCTTAATGCATACTCTCATTG     NA      NA
DQ107935        Macquaria novemaculeata voucher BIOUG<CAN>:BW-A568 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial  45783   Eukaryota       Chordata        Actinopteri     'Percalatidae'  Centrarchiformes        Percalates      Percalates novemaculeata        CCTCTATCTTGTATTTGGTGCCTGGGCCGGAATAGTAGGCACGGCTTTAAGTTTGCTCATTCGAGCAGAGCTTAGCCAGCCAGGCGCCCTCCTTGGGGATGACCAAATTTATAATGTAATTGTTACAGCACATGCATTTGTAATAATTTTCTTTATGGTAATGCCTATCATAATTGGGGGCTTTGGAAACTGACTCATCCCCCTTATGATCGGTGCCCCTGATATAGCTTTCCCTCGCATAAATAATATAAGCTTTTGACTTCTCCCCCCCTCTTTCCTGCTTCTCCTTGCTTCTTCTGGAGTAGAGGCTGGTGCCGGAACCGGGTGAACAGTGTATCCGCCCCTAGCAGGCAATTTAGCTCACGCAGGAGCATCTGTTGATCTAACCATCTTCTCCCTTCATCTAGCAGGGGTTTCCTCAATTCTTGGGGCCATTAACTTCATCACTACTATTATTAACATAAAGCCTCCAGCTACTTCTCAATATCAAACCCCCCTATTCGTGTGAGCAGTTCTGATTACCGCTGTCCTTCTTCTCCTTTCCCTCCCAGTCCTTGCCGCTGGTATTACAATACTACTCACAGATCGTAATCTTAACACTACCTTTTTTGACCCCGCGGGGGGAGGAGACCCAATTCTCTATCAGCACTTGTTC NA      NA