Nonmetric multidimensional scaling (NMDS) is a powerful statistical tool which enables complex multivariate data sets to be visualized in a reduced number of dimensions. Users typically evaluate the fit of an NMDS ordination via ordination “stress” (i.e., data distortion) against a commonly accepted set of heuristic guidelines. However, these guidelines do not account for the mathematical relationship which links ordination stress to sample size. Consequently, researchers working with large data sets may unnecessarily present ordinations in an intractable number of dimensions, subdivide their data, or forego the use of NMDS entirely and lose the benefits of this highly flexible and useful technique. In order to overcome the limitations of these practices, we advocate for an alternative approach to the evaluation of NMDS ordination fit via the usage of permutation-based ecological null models. We present the rationale for this approach from a theoretical basis, supported by a brief literature review, and an example usage of the methodology. Our literature review shows that NMDS analyses often far exceed the number of observations under which the original stress guidelines were formulated—with a significant increasing trend in recent decades. Adoption of a permutation-based approach will consequently provide a more flexible and quantitative evaluation of NMDS fit and allow for the continued application of NMDS in an era of increasingly large datasets. The trouble with stress Researchers across a diverse array of fields are often tasked with teasing out hidden patterns of structure from within expansive and highly-dimensional datasets. Like many of our peers in ecology and oceanography, our working group often employs nonmetric multidimensional scaling (NMDS) as the method of choice for visualizing patterns of community abundance in a tractable number of dimensions—typically 2 or 3. NMDS is an extremely flexible technique for analyzing many different types of data, especially highlydimensional data that exhibit strong deviations from assumptions of normality. Unlike some other ordination techniques, the NMDS approach fits data to a number of axes that are determined a priori to the analysis and does not contain hidden axes of variation. NMDS analysis can only be achieved through a computationally-dense (and somewhat opaque) algorithm that cannot be performed without the aid of a computer. Consequently, usage is heavily guided by heuristic guidelines and common practices within the field. These common practices guide users to the minimum number of dimensions in which a given dataset can be visualized without inducing unacceptable levels of distortion (measured as ordination “stress”). In preparing some data for a recent publication, we encountered a situation that led us to question these common practices. Specifically, this occurred when we attempted to visualize some plankton community data in a 2-dimensional NMDS ordination, and the resultant value of ordination stress (the de facto metric of ordination fit) exceeded the commonly accepted limit of 0.2 (or 20— depending on how the chosen software scales the stress values) (Kruskal 1964a; Clarke 1993; McCune and Grace 2002). As reviewers of earlier publications have insisted to us that this value be utilized as a strict cutoff, we reran the ordination seeking a 3-dimensional solution with lower stress. Although the resultant ordination achieved a stress value of less than 0.2, the addition of a third dimension provided little to no improvement in interpretative power, and in many ways obscured the major trends in the data. As we consulted the ecological literature, we observed that rigid adherence to this threshold is not uncommon. We found that this threshold was commonly delineated in the methodological details of manuscripts (e.g., see Boyra et al. 2004; Vizzini and Mazzola 2004; Bowen et al. 2005; Heino *Correspondence: eric.dexter@wsu.edu Additional Supporting Information may be found in the online version of this article. 1 LIMNOLOGY and OCEANOGRAPHY: METHODS Limnol. Oceanogr.: Methods 00, 2018, 00–00 VC 2018 Association for the Sciences of Limnology and Oceanography doi: 10.1002/lom3.10257 Limnol. Oceanogr.: Methods 16, 2018, 434–443

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lom3.10257

The trouble with stress: A flexible method for the evaluation of nonmetric multidimensional scaling

Oceanographic Processes in Chilean Fjords of Patagonia: From small to large-scale studies

Role of resting cysts in Chilean Alexandrium catenella dinoflagellate blooms revisited

Fjord systems represent hotspots of primary productivity and organic carbon burial. However, the factors which control the primary production in mid-latitude fjords are poorly understood. In this context, results from the first fine-scale measurements of bio-oceanographic features in the water column of fjords associated with the Strait of Magellan are presented. A submersible fluorescence probe (FP) was used to measure the Chlorophyll- a (Chl- a) concentration in situ, along with conductivity, temperature, hydrostatic pressure (depth) and dissolved oxygen (CTD-O 2 ) of the water column. The Austral spring results of 14 FP-CTD-O 2 profiles were used to define the vertical and horizontal patches of the fluorescent pigment distribution and their spatial relations with respect to the observed hydrographic features. Three zones with distinct water structures were defined. In all zones, the ‘brown’ spectral group (diatoms and dinoflagellates) predominated accounting for >80 wt% of the phytoplankton community. Thin layers with high Chl- a concentr a tion were detected in 50% of the profiles. These layers harbored a substantial amount (30–65 wt%) of the phytoplankton biomass. Stratification was positively correlated to the occurrence of Chl- a thin layers. In stable and highly stratified water columns the integrated Chl- a concentr a tion was higher and frequently located within thin layers whereas well mixed water columns displayed lower values and more homogeneous vertical distribution of Chl- a . These results indicate that mixing/stability processes are important factors accounting to the vertical distribution of Chl- a in Magellan fjords.

Chlorophyll-a thin layers in the Magellan fjord system: The role of the water column stratification

. Coccolithophores are potentially affected by ongoing
ocean acidification, where rising CO 2 lowers seawater pH and calcite
saturation state ( Ωcal ). Southern Patagonian fjords and
channels provide natural laboratories for studying these issues due to high
variability in physical and chemical conditions. We surveyed coccolithophore
assemblages in Patagonian fjords during late spring 2015 and early spring
2017. Surface Ωcal exhibited large variations driven mostly by
freshwater inputs. High- Ωcal conditions (max. 3.6) occurred in
the Archipelago Madre de Dios. Ωcal ranged from 2.0–2.6 in the
western Strait of Magellan and 1.5–2.2 in the inner channel and was
subsaturating (0.5) in Skyring Sound. Emiliania huxleyi was the only coccolithophore widely
distributed in Patagonian fjords ( >  96 % of total
coccolithophores), only disappearing in the Skyring Sound, a semi-closed
mesohaline system. Correspondence analysis associated higher E. huxleyi biomasses with
lower diatom biomasses. The highest E. huxleyi abundances in Patagonia were in the
lower range of those reported in Norwegian fjords. Predominant morphotypes
were distinct from those previously documented in nearby oceans but similar
to those of Norwegian fjords. Moderately calcified forms of E. huxleyi A morphotype were
uniformly distributed throughout Patagonia fjords. The exceptional
R/hyper-calcified coccoliths, associated with low Ωcal values
in Chilean and Peruvian coastal upwellings, were a minor component
associated with high Ωcal levels in Patagonia. Outlying mean
index (OMI) niche analysis suggested that pH and Ωcal conditions
explained most variation in the realized niches of E. huxleyi morphotypes. The
moderately calcified A morphotype exhibited the widest niche breadth
(generalist), while the R/hyper-calcified morphotype exhibited a more
restricted realized niche (specialist). Nevertheless, when considering an
expanded sampling domain, including nearby southeast Pacific coastal and
offshore waters, even the R/hyper-calcified morphotype exhibited a higher
niche breadth than other closely phylogenetically related coccolithophore
species. The occurrence of E. huxleyi in naturally low pH– Ωcal 
environments indicates that its ecological response is plastic and capable
of adaptation.

/pdf/abundances-and-morphotypes-of-the-coccolithophore-emiliania-1ps0ykkbs3.pdf

Abundances and morphotypes of the coccolithophore Emiliania huxleyi in southern Patagonia compared to neighboring oceans and northern-hemisphere fjords

Diatoms and dinoflagellates macroscopic regularities shaped by intrinsic physical forcing variability in Patagonian and Fuegian fjords and channels (48°–56°S)

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Diatoms and dinoflagellates macroscopic regularities shaped by intrinsic physical forcing variability in Patagonian and Fuegian fjords and channels (48°–56°S)