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csmiguel · Mar 8, 2022 · 88a7399 · 88a7399
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diff --git a/README.md b/README.md
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 # Complete mitogenome of the garden dormouse (_Eliomys quercinus_)
 
-Giovanni Forcina, Miguel-Camacho Sanchez, Anna Cornellas, Jennifer Leonard. Complete mitogenome of the garden dormouse (_Eliomys quercinus_): a new resource for the genetic monitoring of a fast-declining European small mammal. submitted.
+Forcina, G., Camacho–Sanchez, M., Cornellas, A., Leonard, J. A., 2022. Complete mitogenomes reveal limited genetic variability in the garden dormouse *Eliomys quercinus* of the Iberian Peninsula. **Animal Biodiversity and Conservation**
 
 ## Mitogenome assembly and annotation
 Adapter trimming and minimal quality filtering on the 3' end were performed with [cutadapt 2.10](https://doi.org/10.14806/ej.17.1.200) using [script1](src/1.trim-fastq.sh).
-A reference mitogenome for _Eliomys quercinus_ was created with [NOVOPlasty3.7](https://doi.org/10.1093/nar/gkw955) using [script2](src/2.novoplasty.sh). The four samples were pooled. NOVOPlasty is able to assembles de-novo mitogenomes using a seed sequence. I used a cytochrome b [GQ453669](data/raw/GQ453669.fasta) from *E. quercinus*. NOVOPlasty was able to reconstruct a single [contig](output/log_eliomys_novoplasty.txt) with the expected size of the mitogenome.
+A reference mitogenome for _Eliomys quercinus_ was created with [NOVOPlasty3.7](https://doi.org/10.1093/nar/gkw955) using [script2](src/2.novoplasty.sh). The four samples were pooled. NOVOPlasty is able to assemble de-novo mitogenomes using a seed sequence. I used a cytochrome b [GQ453669](data/raw/GQ453669.fasta) from *E. quercinus*. NOVOPlasty was able to reconstruct a single [contig](output/log_eliomys_novoplasty.txt) with the expected size of the mitogenome.
 
 Individual samples of *Eliomys* were mapped to the reference mitogenome using [BWA mem 0.7.12-r1039](https://arxiv.org/abs/1303.3997). [SAMtools 1.3](https://doi.org/10.1093/bioinformatics/btp352) (using htslib 1.3), was used to discard reads with quality mapping below 40 and remove PCR duplicates, with [script3](src/3.assemble.sh).
 
-~~Mitogenomes were annotated using the annotation module from MitoZ using [script4](src/4.annotate-mitogenomes.sh)~~ **UPDATE**: mitogenomes were annotated with [MITOS2 webserver](http://mitos.bioinf.uni-leipzig.de/index.py). [MITOS](https://doi.org/10.1016/j.ympev.2012.08.023) provided better annotations compared to MitoZ. The annotations have been manually curated after comparing them with the NCBI staff-curated mitochondrial genomes of two close species: _Muscardinus avellanarius_ - [NC_050264](https://www.ncbi.nlm.nih.gov/nuccore/NC_050264) and _Glis glis_ - [NC_001892.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_001892).
+Mitogenomes were annotated with [MITOS2 webserver](http://mitos.bioinf.uni-leipzig.de/index.py). [MITOS](https://doi.org/10.1016/j.ympev.2012.08.023) provided better annotations compared to MitoZ. The annotations have been manually curated after comparing them with the NCBI staff-curated mitochondrial genomes of two close species: _Muscardinus avellanarius_ - [NC_050264](https://www.ncbi.nlm.nih.gov/nuccore/NC_050264) and _Glis glis_ - [NC_001892.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_001892).
 
 ## Reconstruction of haplotype networks using cytochrome b
-All cytochrome b sequences from _E. quercinus_ available in genbank were retrieved with the [rentrez]( https://doi.org/10.7287/peerj.preprints.3179v2) R package using [script5](src/5.retrieve-cytb.R). They were combined with assembled cytb sequences using [script6](src/6.multifasta-cytb.sh) and written to a fasta.
+All *cytochrome b* sequences from _E. quercinus_ available in GenBank were retrieved with the [rentrez]( https://doi.org/10.7287/peerj.preprints.3179v2) R package using [script5](src/5.retrieve-cytb.R). They were combined with assembled cytb sequences using [script6](src/6.multifasta-cytb.sh) and written to a fasta.
 
-Using [script7](src/7.msa-trim.sh), cytb sequences were aligned using [mafft v7.453](https://doi.org/10.1093/molbev/mst010). The resulting MSA was trimmed using [trimAl v1.4.rev15 build 2013-12-17](https://doi.org/10.1093/bioinformatics/btp348) to remove sequences and positions in the MSA to maximize the amount of information. The MSA was converted to nexus using [AMAS](https://doi.org/10.7717/peerj.1660).
+Using [script7](src/7.msa-trim.sh), *cytb* sequences were aligned using [mafft v7.453](https://doi.org/10.1093/molbev/mst010). The resulting MSA was trimmed using [trimAl v1.4.rev15 build 2013-12-17](https://doi.org/10.1093/bioinformatics/btp348) to remove sequences and positions in the MSA to maximize the amount of information. The MSA was converted to nexus using [AMAS](https://doi.org/10.7717/peerj.1660).
 Final haplotype networks were reconstructed with [PopArt](https://doi.org/10.1111/2041-210X.12410), using the TCS algorithm. The msa NEXUS file is available in [output/cyb-network.nex](output/cyb-network.nex).
 
 ## Phylogenetic reconstructions
-A maximum likelihood tree was reconstructed with 1st and 2nd codon positions of protein-coding genes from all mitogenomes of Gliridae available in GenBank. Initial trees with Sciuridae included lots of saturated positions. I tried then a ML tree with only dormice and *Glis glis* as basal to all of them, as in [Upham et al. 2019](https://doi.org/10.1371/journal.pbio.3000494). The [final tree](output/RAxML_bipartitions.mito.tree) was produced following [these steps](src/mitogenomes_ML.txt) and [this DNA alignment](raxml.phy).
+A maximum likelihood tree was reconstructed with 1st and 2nd codon positions of protein-coding genes from all mitogenomes of Gliridae available in GenBank. Initial trees with Sciuridae included lots of saturated positions. I tried then a ML tree with only dormice and *Glis glis* as sister to all of them, as in [Upham et al. 2019](https://doi.org/10.1371/journal.pbio.3000494). The [final tree](output/RAxML_bipartitions.mito.tree) was produced following [these steps](src/mitogenomes_ML.txt) and [this DNA alignment](data/mitogenomes_ML/raxml.phy).
 
 ## Annotated mitochondrial genomes
 Mitogenomes were deposited in GenBank under the BioProject [PRJNA727082](https://www.ncbi.nlm.nih.gov/bioproject/727082): Genetic resources for small mammals.

diff --git a/output/eliomys.filt.fasta-out.pdf b/output/eliomys.filt.fasta-out.pdf
diff --git a/output/formatted_tree_giovanni b/output/formatted_tree_giovanni
diff --git a/output/formatted_tree_giovanni.png b/output/formatted_tree_giovanni.png
diff --git a/src/distribution_gbif.r b/src/distribution_gbif.r
@@ -1,3 +1,6 @@
+# (c) Miguel Camacho Sánchez
+# https://orcid.org/0000-0002-6385-7963
+# github.com/csmiguel/eliomys
 #######################################
 ## DOWNLOAD AND CLEAN DATA FROM GBIF ##
 #######################################

diff --git a/src/meta.r b/src/meta.r
@@ -1,3 +1,7 @@
+# (c) Miguel Camacho Sánchez
+# https://orcid.org/0000-0002-6385-7963
+# github.com/csmiguel/eliomys
+# create meta data table
 meta <- data.frame(
   stringsAsFactors = FALSE,
   sample = c("AJ225030","FM164278","FR848957",

diff --git a/src/mitogenomes_ML.txt → src/steps2mitogenomeML.txt b/src/mitogenomes_ML.txt → src/steps2mitogenomeML.txt