Update main.tex

16S rRNA explanation

papers/Gagnon_Kebe_Tahiri/main.tex

@@ -68,7 +68,7 @@ \subsection{Data pre-processing}
 
 The habitat and water mass of the sampling points are the only attributes taken directly via Table 1 of \citep{uhlir_adding_2021}. Thus, the definitions of water bodies described by \citep{hansen_north_2000, brix2010distribution, ostmann_marine_2014} were used as a reference for the GIN seas around Iceland: Arctic Polar Water (APW, $n=15$), Iceland Sea Overflow Water (ISOW, $n=15$), North Atlantic Water (NAW, $n=9$), Arctic Polar Water/Norwegian Sea Arctic Intermediate Water (APW/NSAIW, $n=7$), warm Norwegian Sea Deep Water (NSDWw, $n=8$), Labrador Sea Water (LSW, $n=3$), cold Norwegian Sea Deep Water (NSDWc, $n=3$), and Norwegian Sea Arctic Intermediate Water (NSAIW, $n=2$) (see Figure \ref{fig:fig3}). In terms of habitat, we considered the three categories used in \citep{uhlir_adding_2021}: deep sea ($n=38$), shelf ($n=15$), and slope ($n=9$) (see Figure \ref{fig:fig4}).
 
-To better interpret the relation and evolutionary responses of benthic species, genetic data are needed \citep{wilson_speciation_1987, uhlir_adding_2021}. Thus, the aligned DNA sequence of the mitochondrial 16S rRNA gene region of each of the samples is included in our analyses. We considered 62 of the 306 aligned DNA sequences that were used for phylogenetic analyses by \citep{uhlir_adding_2021}. Since some of the specimens in our sample have their DNA sequence duplicated, or even quadrupled with a difference of one to two nucleotides, we considered the longest-aligned DNA sequence of each specimen. Figures \ref{fig:fig1}, \ref{fig:fig2}, \ref{fig:fig5} and \ref{fig:fig6} were made using Python 3.11, while Figures \ref{fig:fig3} and \ref{fig:fig4} were made using RStudio Desktop 4.3.2.
+To better interpret the relation and evolutionary responses of benthic species, genetic data are needed \citep{wilson_speciation_1987, uhlir_adding_2021}. Thus, the aligned DNA sequence of the mitochondrial 16S rRNA gene region of each of the samples is included in our analyses. The 16S rRNA region was chosen because not only is it standard in phylogeny and phylogeography studies \citep{hugenholtz1998impact}, but it is sufficiently conserved over time to ensure exact alignments between different species or populations \citep{saccone1999evolutionary}. We considered 62 of the 306 aligned DNA sequences that were used for phylogenetic analyses by \citep{uhlir_adding_2021}. Since some of the specimens in our sample have their DNA sequence duplicated, or even quadrupled with a difference of one to two nucleotides, we considered the longest-aligned DNA sequence of each specimen. Figures \ref{fig:fig1}, \ref{fig:fig2}, \ref{fig:fig5} and \ref{fig:fig6} were made using Python 3.11, while Figures \ref{fig:fig3} and \ref{fig:fig4} were made using RStudio Desktop 4.3.2.
 
 \subsection{\textit{aPhyloGeo} software}