title: scipy hierarchy.linkage and Bray-Curtis distances not consistent
body: <p>I am working with a set of species counts (counts) from several different sample stations (stations). I have calculated the Bray-Curtis similarity between every possible pair of sample stations using the pw_distance function from scikit-bio. This produces a distance matrix with values bounded between 0 and 1. So far so good.</p>
  
  <p>I want to use that distance matrix to produce a dendrogram showing how the sample stations cluster together. I am doing this using scipy's hierachy.linkage function to find the linkages for the dendrogram, and then plotting with hierarchy.dendrogram.</p>
  
  <p>Here's my code:</p>
  
  <pre><code>from skbio.diversity.beta import pw_distances
  from scipy.cluster import hierarchy
  
  bc_dm = pw_distances(counts, stations, metric = "braycurtis")
  
  # use (1 - bc_dm) to get similarity rather than dissimilarity
  sim = 1 - bc_dm.data
  
  Z = hierarchy.linkage(sim, 'ward')
  hierarchy.dendrogram(
      Z,
      leaf_rotation=0.,  # rotates the x axis labels
      leaf_font_size=10.,  # font size for the x axis labels
      labels=bc_dm.ids,
      orientation="left"
  )
  </code></pre>
  
  <p><a href="https://i.stack.imgur.com/Nxd1U.png" rel="nofollow noreferrer">here is a link to the dendrogram produced by the above code</a></p>
  
  <p>As I understand it, the distance on the dendrogram should correspond to the Bray-Curtis similarity (analogous to a distance), but the distance values on my dendrogram reach a maximum of over 30. Is this correct? If not, how can I scale my distances to correspond to the Bray-Curtis similarity between sample stations? If it is correct, what do the distances on teh dendrogram really correspond to?</p>