## 2 Methods: Modelling Approach
### Equivalent Algal Populations Model: Principal Attributes  
The EAP model has been used for a variety of applications [35; 37; 63; 64]. It can be assumed that a model demonstrated as successful in phytoplankton-dominated waters [65] addresses the phytoplankton component accurately. Models designed for low biomass, with simplistic and absorption-decoupled phytoplankton scattering models, tend to underperform in higher biomass conditions when phytoplankton IOPs dominate [65]. It follows that the phytoplankton component of the combined optical properties is not generally well represented in these models. Following a reductionist approach, good information on the phytoplankton component is a prerequisite for any quantitative comment on the optical contribution of respective PFTs, or identifying changes in the bulk optical properties of seawater as dominant PFTs change. Only when representing the detailed nature of phytoplankton optics, with absorption and scattering biophysically consistent--as they are in nature--is a causal understanding of their interactive effect on the optical signal possible [66; 32]. The EAP model exhibits a two-layered sphere particle and equivalent size-based community structure [27], which enables the calculation of phytoplankton IOPs from first principles, presenting a valuable opportunity for furthering the understanding of causal relationships between phytoplankton physiology and their optical characteristics based on quantified community structure. It is emphasised that this is not an empirical model and its use here is not to provide optical closure, but rather to identify and understand the biophysical drivers of phytoplankton optics and their contribution to an observable signal in the context of different water types. At the core of the model are the phytoplankton particle refractive indices, with the imaginary part of the refractive index approximately representing that portion of light that is absorbed by the cell, and the real part of the refractive index representing that portion of light which is scattered. The imaginary and real parts of the refractive index spectra are numerically linked through the Kramers-Kronig relations [67], whereby the real part of the refractive index \(n(\lambda)\) is calculated as the imaginary part of a Hilbert transform of the imaginary refractive index, originally derived from cellular absorption measurements. It should be noted that the imaginary refractive index characterises the absorption of the intracellular material and has no dependency on cell size. This has implications for the applicability of the model to a wide range of cell sizes, and is discussed further in Appendix A.1. With a real refractive index of 1.12 for the 'chloroplast' sphere, and as 1.02 for the 'cytoplasm' sphere, this yields an overall particle spectral real refractive index of between 1.03 and 1.04 for phytoplankton cells (see also [PERSON] et al. [32], [PERSON] [68]). Full details of the refractive index calculations can be found in [PERSON] et al. [69]. In this model, the imaginary part of the refractive index is also numerically linked to the specified intracellular Chl \(a\) concentration [27; 52; 54; 55; 70]. For eukaryotic particles, a core sphere represents the cytoplasm (which contains approximately 80% water, and is almost colourless), while an outer sphere represents the more refractive chloroplast, where the pigmented material (generally Chl \(a\) in the largest part) is also strongly absorbing. A critical feature of the model is that Chl \(a\)-specific absorption (a*\(\phi\)) is constrained at 675 nm to reflect the theoretical maximum absorption by unpackaged phytoplankton of 0.027 mg/m\({}^{2}\) as per [PERSON] et al. [71].