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6.4. Results 83
employed indirect gradient analysis (see [Ramette, 2007] for a review
of multivariate analyses) after [Virtanen et al., 2006] to relate DUF
abundances in network II (Fig. 6.1; 17 DUF varieties) to chlorophyll
concentrations at appropriate GOS sites (n=56; see Supplementary
methods online). We standardized DUF abundances at each site by
the median abundance of 22 ‘single-copy domains’ detected at that
site.
Figure 6.2: Hypothesis contextualization using indirect gradient analysis of GOS sites described
by the abundances of DUFs in Network II (ref. Fig. 6.1) and chlorophyll concentration data.
Each bubble represents one GOS site and bubble size reflects the in situ chlorophyll concentration
measured during the expedition. Bubble positions reflect the Bray-Curtis dissimilarity
between sites calculated from the per site abundance profiles of DUFs in Network II. The
blue vector describes the linear fit of chlorophyll concentration data to the ordination (Rv
2 ≈ 0.52, P (> R) ≈ 9.99 × 10 − 4). Red isoclines describe a generalized additive model fit of
the same chlorophyll data to the ordination (Rs 2 ≈ 0.91, p ≈ 2.00 × 10 − 16) and are labeled
with the corresponding chlorophyll concentration (in 4µg chlorophyll per kg seawater). Regions
where the chlorophyll isoclines and vector intersect perpendicularly suggest a coherent response
gradient of metagenomic DUF content to chlorophyll concentrations.
We then ordinated sites by non-metric dimensional scaling (NMDS;
Fig. 6.2, hollow circles) using Bray-Curtis dissimilarities. Next, we