\documentclass[tikz]{standalone}
\usepackage{tikz}
\usepackage{xcolor}

\definecolor{lightorange}{HTML}{E69F00}
\definecolor{darkorange}{HTML}{D55E00}
\definecolor{lightblue}{HTML}{56B4E9}
\definecolor{darkblue}{HTML}{0072B2}


\usetikzlibrary{trees, positioning, shapes, calc, fit}

\begin{document}

\begin{tikzpicture}[
        level distance=1.5cm,
        level 1/.style={sibling distance=4cm},
        level 2/.style={sibling distance=1.5cm},
        every node/.style={circle, draw, minimum size=6mm},
        edge from parent/.style={draw, -latex}
    ]

    % ======================
    % ARBRE PHYLOGENETIQUE
    % ======================

    \node (root) {$i=0$}
    child {
            node[fill=lightorange] {$i=1$}
            child { node[fill=darkorange] {$i=3$} }
            child { node[fill=darkorange] {$i=4$} }
            child { node[fill=darkorange] {$i=5$} }
        }
    child {
            node[fill=lightblue] {$i=2$}
            child { node[fill=darkblue] {$i=6$} }
            child { node[fill=darkblue] {$i=7$} }
        };

    % Labels des niveaux

    \node[left=1cm of root-1-1,draw=none] (l2) {$l=2$};
    \node[above=0.4cm of l2,draw=none] (l1) {$l=1$};
    \node[above=0.4cm of l1,draw=none] (l0) {$l=0$};

    % ======================
    % ESPACE LATENT (droite)
    % ======================

    \begin{scope}[xshift=6cm, yshift=-3.5cm]

        % Axes
        \draw[->] (-0.5,0) -- (4,0) node[right,draw=none] {};
        \draw[->] (0,-0.5) -- (0,4) node[above,draw=none] {};

        % Points correspondant aux noeuds
        \node[inner sep=1.5pt] (g0) at (2,2) {$\gamma_{0,0}$};

        \node[inner sep=1.5pt, left of = g0, fill = lightorange] (g11) {$\gamma_{1,1}$};
        \node[inner sep=1.5pt, right of = g0, fill = lightblue] (g12) {$\gamma_{1,2}$};

        \node[inner sep=1.5pt, above  = 0.5cm of g11, fill=darkorange]  (g23) {$\gamma_{2,3}$};
        \node[inner sep=1.5pt, above right = 0.1cm of g23, fill=darkorange]  (g24) {$\gamma_{2,4}$};
        \node[inner sep=1.5pt, below = 0.5cm of g11, fill=darkorange]  (g25) {$\gamma_{2,5}$};

        \node[inner sep=1.5pt, right = 0.05 cm of g25, fill=darkblue] (g26) {$\gamma_{2,6}$};
        \node[inner sep=1.5pt, above of = g12, fill=darkblue] (g27) {$\gamma_{2,7}$};

        \path (g0) edge[densely dotted] (g11) edge[densely dotted] (g12);
        \path (g11) edge[densely dotted] (g23) edge[densely dotted] (g24) edge[densely dotted] (g25);
        \path (g12) edge[densely dotted] (g27) edge[densely dotted] (g26);

        \node [inner xsep=6pt, inner ysep=3pt, draw = black, fit={(g25) (g26)}, rectangle] {};
    \end{scope}

\end{tikzpicture}

\end{document}