DOI: 10.5061/dryad.76j14s5
title: Data from: Evolution of vertebrate nicotinic acetylcholine receptors

description: Background: Many physiological processes are influenced by nicotinic
 acetylcholine receptors (nAChR), ranging from neuromuscular and
 parasympathetic signaling to modulation of the reward system and long-term
 memory. Due to the complexity of the nAChR family and variable
 evolutionary rates among its members, their evolution in vertebrates has
 been difficult to resolve. In order to understand how and when the nAChR
 genes arose, we have used a broad approach of analyses combining
 sequence-based phylogeny, chromosomal synteny and intron positions.
 Results: Our analyses suggest that there were ten subunit genes present in
 the vertebrate predecessor. The two basal vertebrate tetraploidizations
 (1R and 2R) then expanded this set to 19 genes. Three of these have been
 lost in mammals, resulting in 16 members today. None of the ten ancestral
 genes have kept all four copies after 2R. Following 2R, two of the
 ancestral genes became triplicates, five of them became pairs, and three
 seem to have remained single genes. One triplet consists of CHRNA7, CHRNA8
 and the previously undescribed CHRNA11, of which the two latter have been
 lost in mammals but are still present in lizards and ray-finned fishes.
 The other triplet consists of CHRNB2, CHRNB4 and CHRNB5, the latter of
 which has also been lost in mammals. In ray-finned fish the neuromuscular
 subunit gene CHRNB1 underwent a local gene duplication generating
 CHRNB1.2. The third tetraploidization in the predecessor of teleosts (3R)
 expanded the repertoire to a total of 31 genes, of which 27 remain in
 zebrafish. These evolutionary relationships are supported by the
 exon-intron organization of the genes. Conclusions: The tetraploidizations
 explain all gene duplication events in vertebrates except two. This
 indicates that the genome doublings have had a substantial impact on the
 complexity of this gene family leading to a very large number of members
 that have existed for hundreds of millions of years.
description: aLRT SH-like trees
 paralogon 1Phylogenetic aLRT
 SH-like trees of the neighboring gene families included in analysis of
 nAChR paralogon 1. There is one neighboring gene family per page in
 alphabetical order. Taxa ID and sequence information details are provided
 in the table below.Table paralogon
 1Table containing
 information about the nAChR neighboring gene families included in the
 analysis of the nAChR paralogon 1. First, information about genome
 assembly versions used are listed, then the following information about
 the neighboring gene families is provided: species, HGNC/ZFIN/Flybase
 symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI
 accession number, taxa ID and additional comments regarding sequence
 update date on NCBI or if there has been manual edits of the original
 Ensembl or NCBI sequence. There is one page per family, presented in
 alphabetical order.aLRT SH-like trees
 paralogon 3Phylogenetic aLRT
 SH-like tree of the neighboring gene families included in analysis of
 nAChR paralogon 3. There is one neighboring gene family per page in
 alphabetical order. Taxa ID and sequence information details are provided
 in the table below.Table paralogon
 3Table containing
 information about the nAChR neighboring gene families included in the
 analysis of the nAChR paralogon 3. First, information about genome
 assembly versions used are listed, then the following information about
 the neighboring gene families is provided: species, HGNC/ZFIN/Flybase
 symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI
 accession number, taxa ID and additional comments regarding sequence
 update date on NCBI or if there has been manual edits of the original
 Ensembl or NCBI sequence. There is one page per family, presented in
 alphabetical order.aLRT SH-like trees
 paralogon 5Phylogenetic aLRT
 SH-like tree of the neighboring gene families included in analysis of
 nAChR paralogon 5. There is one neighboring gene family per page in
 alphabetical order. Taxa ID and sequence information details are provided
 in the table below.Table paralogon
 5Table containing
 information about the nAChR neighboring gene families included in the
 analysis of the nAChR paralogon 5. First, information about genome
 assembly versions used are listed, then the following information about
 the neighboring gene families is provided: species, HGNC/ZFIN/Flybase
 symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI
 accession number, taxa ID and additional comments regarding sequence
 update date on NCBI or if there has been manual edits of the original
 Ensembl or NCBI sequence. There is one page per family, presented in
 alphabetical order.aLRT SH-like trees
 paralogon 1 in teleostsPhylogenetic aLRT
 SH-like tree of the neighboring gene families included in analysis of
 nAChR paralogon 1 in relation to 3R in teleosts. There is one neighboring
 gene family per page in alphabetical order. Taxa ID and sequence
 information details are provided in the table below.Table paralogon 1 in
 teleostsTable containing
 information about the nAChR neighboring gene families included in the
 analysis of nAChR paralogon 1 in relation to 3R event in teleosts. First,
 information about genome assembly versions used are listed, then the
 following information about the neighboring gene families is provided:
 species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold
 position, Ensembl ID or NCBI accession number, taxa ID and additional
 comments regarding sequence update date on NCBI or if there has been
 manual edits of the original Ensembl or NCBI sequence. There is one page
 per family, presented in alphabetical order.Maximum likelihood tree
 nAChR gene familyThe phylogenetic maximum
 likelihood tree of the nAChR genes in nexus format. The tree topology is
 supported by a non-parametric Ultra-Fast Bootstrap (UFBoot) and
 approximate Likelihood-Ratio Test (aLRT) with 1000 replicates. For
 simplicity only UFBoot values are shown. The taxa ID contains the species,
 the localization of the gene (chromosome/scaffold/contig number) and a
 number indicating the order on the chromosome/scaffold/contig if several
 genes are located on the same one. The taxa ID of human and zebrafish
 genes with annotated HGNC or ZFIN names, respectively, also contain these
 names. The assigned taxa ID and sequence information details are provided
 in Additional file 4.