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papers/Gagnon_Kebe_Tahiri/main.tex

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 \begin{abstract}
-The peracarid taxon Cumacea is an essential indicator of benthic quality in marine ecosystems. This study investigated the influence of environmental (i.e., biological or ecosystemic), climatic (i.e., meteorological or atmospheric), and spatial (i.e., geographic or regional) variables on their genetic adaptability in the Northern North Atlantic, focusing on Icelandic waters. We analyzed partial sequences of the 16S rRNA mitochondrial gene from 62 Cumacea specimens. Using the \textit{aPhyloGeo} software, we compared these sequences with relevant parameters such as latitude (decimal degree) at the end of sampling, wind speed (m/s) at the start of sampling, O\textsubscript{2} concentration (mg/L), and depth (m) at the start of sampling.
+The peracarid taxon Cumacea is an essential indicator of benthic quality in marine ecosystems. This study investigated the influence of environmental (i.e., biological or ecosystemic), climatic (i.e., meteorological or atmospheric), and spatial (i.e., geographic or regional) variables on their genetic adaptability in the Northern North Atlantic, focusing on Icelandic waters. We analyzed partial sequences of the 16S rRNA mitochondrial gene from 59 Cumacea specimens. Using the \textit{aPhyloGeo} software, we compared these sequences with relevant parameters such as latitude (decimal degree) at the end of sampling, wind speed (m/s) at the start of sampling, O\textsubscript{2} concentration (mg/L), and depth (m) at the start of sampling.
 
 Our analyses revealed variability in most spatial and biological variables, reflecting the diversity of ecological requirements and benthic habitats. The most common Cumacea families, Diastylidae and Leuconidae, suggest adaptations to various marine environments. Phylogeographic analysis showed a divergence between specific genetic sequences and two habitat variables: wind speed (m/s) at the start of sampling and O\textsubscript{2} concentration (mg/L). This may suggest potential divergent local adaptation to these fluctuating conditions.
 
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 \end{abstract}
 
 \section{Introduction}\label{introduction}
-The North Atlantic and Subarctic regions, particularly the Icelandic waters, are of ecological interest due to their diverse water masses and unique oceanographic features \citep{schnurr_composition_2014, meisner_benthic_2014, uhlir_adding_2021}. These areas form vital {benthic habitats}\footnote{These are areas on the bottom of the oceans or lakes, including sediments and organisms that live in them.} \citep{levin2009ecological} and enhance our understanding of deep-sea ecosystems and biodiversity patterns \citep{rogers2007corals, danovaro2008exponential, uhlir_adding_2021}. The IceAGE project and its predecessors, BIOFAR and BIOICE, provide invaluable data for studying the impacts of climate change and seabed mining, especially in the Greenland, Iceland, and Norwegian (GIN) seas \citep{meisner_prefacebiodiversity_2018}.
+The North Atlantic and Subarctic regions, particularly the Icelandic waters, are of ecological interest due to their diverse water masses and unique oceanographic features \citep{schnurr_composition_2014, meisner_benthic_2014, uhlir_adding_2021}. These areas form vital {benthic habitats}\footnote{Areas at the bottom of oceans, lakes, or rivers, including sediments and organisms that live in them.} \citep{levin2009ecological} and enhance our understanding of deep-sea ecosystems and biodiversity patterns \citep{rogers2007corals, danovaro2008exponential, uhlir_adding_2021}. The IceAGE project and its predecessors, BIOFAR and BIOICE, provide invaluable data for studying the impacts of climate change and seabed mining, especially in the Greenland, Iceland, and Norwegian (GIN) seas \citep{meisner_prefacebiodiversity_2018}.
 
-Cumacea, a crustacean taxon within Peracarida, provide major indicators of marine ecosystem health due to their sensitivity to environmental fluctuations \citep{stransky_diversity_2010} and their contribution to benthic food webs \citep{rehm2009cumacea}. Despite their ecological importance, deep-sea benthic invertebrates’ evolutionary history remains uncharted, notably in the North Atlantic \citep{jennings_phylogeographic_2014}. Interpretation of the genetic distribution and demography of these deep-sea organisms is essential to predict their response to climate change \citep{jennings_phylogeographic_2014} and anthropogenic pressures (e.g., seabed mining) \citep{meisner_prefacebiodiversity_2018}, and to improve our knowledge of their adaptive mechanisms in these deep-sea ecosystems.
+Cumacea, a crustacean taxon within Peracarida, provide major indicators of marine ecosystem health due to their sensitivity to environmental fluctuations \citep{stransky_diversity_2010} and their contribution to benthic food webs \citep{rehm2009cumacea}. Despite their ecological importance, deep-sea benthic invertebrates’ evolutionary history remains uncharted, notably in the North Atlantic \citep{jennings_phylogeographic_2014}. Studying and interpreting the genetic and demographic patterns of these deep-sea organisms is essential for predicting their response to climate change \citep{jennings_phylogeographic_2014} and anthropogenic pressures \citep{meisner_prefacebiodiversity_2018}, and for improving our knowledge of their adaptive mechanisms in these deep-sea ecosystems.
 
-Given the urgency of the above factors, this study aims to analyze the influence of ecological (climatic and environmental) and spatial parameters on the genetic adaptability of Cumacea in the Northern North Atlantic. More specifically, we will examine whether genetic adaptation exists between the genetic structure of a region of a partial sequence of the 16S rRNA mitochondrial gene of the Cumacea species sampled and their habitat parameters. We will determine which variables diverge most from a specific sequence of this partial genetic sequence (i.e., a window) and further explore the potential associated protein using bioinformatics tools to interpret its biological relevance. Our approach includes confirming different {phylogeographic models}\footnote{Phylogeographic models are computational tools that analyze relationships between the genetic structures of populations and their geographic distributions. In our case, by incorporating regional, biological, and atmospheric characteristics, we can interpret their impact on the genetic distribution of Cumacea species.} and updating a Python package (currently in beta), \textit{aPhyloGeo}, to simplify these analyses.
+Given the urgency of the above factors, this study aims to analyze the influence of ecological (climatic and environmental) and spatial variables on the genetic adaptability of Cumacea in the Northern North Atlantic. More specifically, we will examine whether there is a genetic adaptation between the genetic structure of a region of a partial sequence of the 16S rRNA mitochondrial gene of the Cumacea species included in our analyses and their habitat parameters. If so, we will determine which variables diverge most from a specific sequence (i.e., window) of this partial sequence and further explore the potential associated protein using bioinformatics tools to interpret its biological relevance. Our approach includes confirming different {phylogeographic models}\footnote{Phylogeographic models are computational tools that analyze relationships between the genetic structures of populations and their geographic distributions. In our case, by incorporating regional, biological, and atmospheric variables, we can analyze and interpret their impact on the genetic adaptation and spatial distribution of Cumacea species.} and updating a Python package (currently in beta), \textit{aPhyloGeo}, to simplify these analyses.
 
 This paper is organized as follows: \autoref{related-works} reviews pertinent studies on the biodiversity and biogeography of deep-sea benthic invertebrates; \autoref{contribution} summarizes the aims and contributions of this study, highlighting aspects relating to the conservation and adaptation of marine invertebrates to climate change; \autoref{materials-methods} describes data collection, preprocessing and phylogeographic analyses of partial genetic sequence and habitat variables; \autoref{metrics} describes the metrics used to evaluate the phylogeographic models; \autoref{results} presents the results; finally, \autoref{conclusion} discusses their implications for future research and conservation efforts.