From 377121284a783a95c6169ad8c1f50904c5d67dde Mon Sep 17 00:00:00 2001 From: JustGag <158193589+JustGag@users.noreply.github.com> Date: Tue, 22 Oct 2024 19:01:22 -0400 Subject: [PATCH] Update main.tex Corrections conclusions --- papers/Gagnon_Kebe_Tahiri/main.tex | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/papers/Gagnon_Kebe_Tahiri/main.tex b/papers/Gagnon_Kebe_Tahiri/main.tex index 6787c42d90..93abb5354c 100644 --- a/papers/Gagnon_Kebe_Tahiri/main.tex +++ b/papers/Gagnon_Kebe_Tahiri/main.tex @@ -251,7 +251,7 @@ \subsubsection{Robinson-Foulds distance}\label{RF} \subsubsection{Normalized Robinson-Foulds distance}\label{RFnorm} The normalized Robinson-Foulds (nRF) distance scales the RF distance to account for the size variations in the trees (number of clades; i.e., a group of species with a common origin), allowing a more equitable comparison. It scales the distance to a range between 0 and 1. In our context, the distance has been normalized by $2n-6$, where $n$ represents the number of taxa (see Equation \eqref{eq:rf_norm} and the last line of code in \autoref{lst:robinsonFoulds}). -Since the size of environmental trees constructed with O\textsubscript{2} concentration data (mg/L) differs from that of other variables due to missing data ($n=3$), this nRF distance allows its dissimilarity with genetic trees to be compared more fairly \citep{tahiri2018new, koshkarov_phylogeography_2022}. It reveals the relative influence of O\textsubscript{2} concentration (mg/L) on Cumacea phylogenetic relationships, independent of tree size \citep{tahiri2018new, koshkarov_phylogeography_2022}. A high distance of a specific window in the nRF distance analysis suggests that we cannot conclude that there is a correlation between this DNA sequence and the variable. It may indicate a topological dissimilarity between the habitat variable trees and the genetic trees at that position in the DNA sequence alignments. +Since the size of environmental trees constructed with O\textsubscript{2} concentration data (mg/L) differs from that of other variables due to missing data, this nRF distance allows its dissimilarity with genetic trees to be compared more fairly \citep{tahiri2018new, koshkarov_phylogeography_2022}. It reveals the relative influence of O\textsubscript{2} concentration (mg/L) on Cumacea phylogenetic relationships, independent of tree size \citep{tahiri2018new, koshkarov_phylogeography_2022}. A high distance of a specific window in the nRF distance analysis suggests that we cannot conclude that there is a correlation between this DNA sequence and the variable. It may indicate a topological dissimilarity between the habitat variable trees and the genetic trees at that position in the DNA sequence alignments. \begin{equation}\label{eq:rf_norm} \text{RF}_{\text{norm}}(T_1, T_2) = \frac{| \Sigma(T_1) \Delta \Sigma(T_2) |}{| \Sigma(T_1) | + | \Sigma(T_2) |} @@ -377,15 +377,15 @@ \section{Results}\label{results} These results provide important insight into the genetic adaptation of Cumacea to their environment. These results need to be analyzed in greater depth to certify their involvement, especially in contrast with \citep{uhlir_adding_2021}, which investigated similar topics of environmental and climatic effects on Cumacea distribution and genetics. The \textit{aPhyloGeo} package is still in the process of being updated. \section{Conclusion}\label{conclusion} -This study examines the effects of meteorological, regional, and ecosystemic variables on the genetics of Cumacea in the waters surrounding Iceland. Our main objective is to determine whether there is a discrepancy between the precise genetic information of the partial 16S rRNA mitochondrial gene sequence (i.e., a window) of Cumacea species and their habitat variables. In addition to data distribution representations (see Figure \ref{fig:fig3}, Figure \ref{fig:fig4}, Figure \ref{fig:fig5} and Figure \ref{fig:fig6}), DNA sequence analyses have identified specific genetic windows that diverge from atmospheric and biological variables such as wind speed (m/s) at the start of sampling (Position in MSA: 560-569 aa; Euclidean distance: 0.86; see Figure \ref{fig:fig7}d) and O\textsubscript{2} concentration (mg/L) (Position in MSA: 1210-1219 aa; Euclidean distance: 1.23; see Figure \ref{fig:fig8}d). These results could mean that these specimens have been shaped by these unique local environments, resulting in genetic sequences adapted to their particular conditions. +This study examines the effects of meteorological, regional, and ecosystemic variables on the genetics of Cumacea in the waters surrounding Iceland. Our main objective is to determine whether there is a discrepancy between the genetic informations of the partial 16S rRNA mitochondrial gene sequence (i.e. a window) of Cumacea species and their habitat variables. In addition to data distribution representations (see Figure \ref{fig:fig3}, Figure \ref{fig:fig4}, Figure \ref{fig:fig5} and Figure \ref{fig:fig6}), DNA sequence analyses, using the \textit{aPhyloGeo} software, have identified specific genetic windows that diverge from atmospheric and biological variables such as wind speed (m/s) at the start of sampling (Position in MSA: 560-569 aa; Euclidean distance: 0.85; see Figure \ref{fig:fig7}d) and O\textsubscript{2} concentration (mg/L) (Position in MSA: 1210-1219 aa; Euclidean distance: 1.23; see Figure \ref{fig:fig8}d). These results could mean that these specimens have been shaped by these unique local environments, resulting in genetic sequences adapted to their particular conditions. -The novelty in our research lies in the exhaustive divergence between habitat variables and genetic mutability in Cumacea, particularly in identifying genetic windows associated with habitat fluctuations, which has not been widely investigated in previous studies \citep{manel2003landscape, vrijenhoek2009cryptic}. In this case, our integrated method identifies specific genetic regions sensitive to ecosystemic and atmospheric variations. Thus, by seeking to determine which of these two variables diverges most with the DNA sequences, the eventual identification of proteins linked to one of these variable DNA sequences will make it possible to represent its functional effects in responses to habitat changes. Our future research will focus on verifying the prediction of this protein and assessing its role in the physiological adaptation of Cumacea to fluctuating conditions, adding a link between genetic data and ecological function. +The novelty in our research lies in the exhaustive divergence between habitat variables and genetic divegence in Cumacea, particularly in identifying genetic windows that diverge from habitat fluctuations, which has not been widely investigated in previous studies \citep{manel2003landscape, vrijenhoek2009cryptic}. Our integrated method identifies specific genetic regions sensitive to ecosystemic and atmospheric variations. Thus, the eventual identification of proteins linked to one of these variable DNA sequences will make it possible to represent its functional effects in responses to habitat changes. Our future research will focus on verifying the prediction of this protein and assessing its role in the physiological adaptation of Cumacea to fluctuating conditions, adding a link between genetic data and ecological function. -Interpreting how marine invertebrates genetically adapt to variations in their habitat can help predict their response to climate change and advance conservation plans to protect them. Identifying the specific variables that influence genetic variability in Cumacea can contribute to the designation and supervision of marine protected areas, assuring they include habitats crucial to the survival and acclimatization of these species. Thus, our results can inform the management of fishing and seabed mining companies by revealing ecologically vulnerable areas where these disturbances can seriously affect benthic biodiversity. +Interpreting how marine invertebrates genetically adapt to variations in their habitat can help predict their response to climate change and advance conservation plans to protect them. Identifying the variables that influence genetic variability in Cumacea can contribute to the designation and supervision of marine protected areas, assuring they include habitats crucial to the survival and acclimatization of these species. Thus, our results can inform the management of fishing and seabed mining companies by revealing ecologically vulnerable areas where these disturbances can seriously affect benthic biodiversity. -Furthermore, our results provide essential knowledge to guide future studies on the genetic adaptation of Cumacea and other invertebrates to ecological and regional variability. Based on these findings, future research should focus on additional ecosystemic and meteorological variables, such as nutrient accessibility, water pH, ocean currents, and the degree of human disturbance, to further improve the interpretation of the complex interactions between genetics and the environment. Extending the scope of application to other marine species, not just marine invertebrates, and various spatial regions would provide a better means of generalizing the results. With this in mind, longitudinal study models on these species could reflect long-term climatic and biological fluctuations and improve our knowledge of the dynamics of genetic acclimatization. +Furthermore, our results provide essential knowledge to guide future studies on the genetic adaptation of Cumacea and other invertebrates to ecological and regional variability. Based on these findings, future research should focus on additional ecosystemic and meteorological variables, such as nutrient accessibility, water pH, ocean currents, and the degree of human disturbance, to further improve the interpretation of the complex interactions between genetics and the environment. Extending the scope of application to other marine species, not just marine invertebrates, and various spatial regions would provide a better means of generalizing the results. With this in mind, longitudinal study models on these different species could reflect long-term climatic and biological fluctuations, and improve knowledge of the dynamics of genetic acclimatization. -However, it is important to recognize the limitations of our study. In particular, the three missing data points on O\textsubscript{2} concentration (mg/L) and the relatively small sample size ($n=62$) may have induced a bias, which could impact the validity of our interpretations and restrict the generalizability of our results. Moreover, these missing data could provide partial insight into the relationship between O\textsubscript{2} concentration (mg/L) and genetic fluctuation in Cumacea, and our sample size may reduce the statistical power of our results. Future studies should address these gaps by incorporating larger sample sizes and more complete datasets to confirm and expand our conclusions. Additionally, as our research focuses solely on the partial sequence of the mitochondrial 16S rRNA gene, utilizing more elaborate genomic methods, such as whole-gene or even whole-genome sequencing, could help better understand marine species' genetic variety and global acclimatization mechanisms. This would provide more comprehensive genetic databases to improve our accuracy and knowledge in identifying existing (and new) marine invertebrate species using DNA barcoding (e.g., mitochondrial DNA cytochrome c oxidase I (COX1)). Finally, multidisciplinary collaborations between ecology, genetics, and oceanography would be essential to enhance knowledge sharing and its application in future research. +However, it is important to recognize the limitations of our study. In particular, the three missing data points on O\textsubscript{2} concentration (mg/L) and the relatively small sample size ($n=62$) may have induced a bias, which could impact the validity of our interpretations and restrict the generalizability of our results. Moreover, these missing data could provide partial insight into the relationship between O\textsubscript{2} concentration (mg/L) and genetic fluctuation in Cumacea, and our sample size may reduce the statistical power of our results. Future studies should address these gaps by incorporating larger sample sizes and more complete datasets to confirm and expand our conclusions. Additionally, as our research focuses solely on the partial sequence of the mitochondrial 16S rRNA gene, utilizing more elaborate genomic methods, such as whole-gene or even whole-genome sequencing, could help better understand marine species' genetic variety and global acclimatization mechanisms. This would provide more comprehensive genetic databases to improve accuracy and knowledge in identifying existing (and new) marine invertebrate species using DNA barcoding (e.g., mitochondrial DNA cytochrome c oxidase I (COX1)). Finally, multidisciplinary collaborations between ecology, genetics, and oceanography would be essential to enhance knowledge sharing and its application in future research. \section{Acknowledgments}\label{acknowledgments} The authors thank the SciPy conference and reviewers for their valuable comments on this paper as well as Mansour Kebe for his technical support and Carolin Uhlir for her clarifications and advice on her study \citep{uhlir_adding_2021}. This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC), the Fonds de recherche du Québec - Nature et technologies (FRQNT), the Université de Sherbrooke grant, and the Centre de recherche en écologie de l’Université de Sherbrooke (CREUS).