Compositional Data Analysis (CoDA) as a tool to study the (paleo)ecology of coccolithophores from coastal-neritic settings off central Portugal
Introduction
Coccolithophores are the predominant phytoplankton group within calcareous nannoplankton, commonly used as (paleo)environmental proxies and markers of oceanographic processes (e.g., Ziveri et al., 2004, Silva et al., 2008, Guerreiro et al., 2013) due to their exceptional fossil record in both open ocean (Ziveri et al., 2004) and continental shelf/slope sediments (Cachão and Moita, 2000, Guerreiro et al., 2005, Guerreiro et al., 2015). Although affected by various post-mortem (biostratonomical) mechanisms, studies indicate that coccolith thanatocoenoses preserved in surface sediments can be closely related to the coccolithophore communities dwelling in the overlaying photic layer (e.g., Abrantes and Moita, 1999, Baumann et al., 2000, Kinkel et al., 2000, Sprengel et al., 2002, Boeckel and Baumann, 2008, Guerreiro et al., 2015) due to rapid transfer mechanisms mediated by zooplankton grazing (Steinmetz, 1994, Balch, 2004). Nevertheless, the correspondence between the coccolithophore living communities and the coccolith species assemblages preserved in the seabed is complex, particularly those close to the coast and in the context of a continental margin dissected by submarine canyons, where both continental and marine factors interplay (see Roth, 1994, Steinmetz, 1994).
Productivity of coccolithophores is primarily a function of light and nutrients, modulated by hydrological parameters like temperature, salinity, turbulence and turbidity (see Margalef, 1978). Seasonal variability in controlling parameters results in successions of seasonally distinct coccolithophore biocoenoses. The coccolith fossil record preserved in the seafloor sediment results from this primary signal, which is further affected by several taphonomical phenomena (i.e., necrolysis, biostratonomy, variations in sediment accumulation rate, bioturbation and diagenesis) that act upon the coccospheres/coccoliths as illustrated in Fig. 1. In other words, whereas a certain productivity represents the cumulative coccolithophore production of a certain region of the ocean, the fossil record is the net cumulative average over 10− 1–104 years of continuous productivity, more or less distorted by taphonomy.
In addition to the primary ecological signal, the coccolith assemblages preserved in seafloor sediments will also contain allochthonous coccolithophores (i.e., advected from adjacent water masses), as well as reworked fossil or subfossil specimens resuspended from the bottom of continental shelf and slope regions. Such contribution is particularly important where continental margins are dissected by submarine canyons, given that these are regions of enhanced water column and sedimentary dynamics (i.e., intensified vertical water motion, internal tides, gravity flows; De Stigter et al., 2007, De Stigter et al., 2011, Oliveira et al., 2007, Arzola et al., 2008).
Once deposited at the seafloor, the coccolith thanatocoenosis will be subjected to the effects of dilution with other sedimentary material (including reworked coccoliths), and to mixing by organisms living in the benthic sediment layer, the latter of which can result in more or less homogenised coccolith taphocoenoses. After burial, the association will be further subjected to diagenesis occurring on longer time scales (i.e., 102–106 years). Processes such as dissolution and recrystallization will tend to preferentially eliminate the smaller and more delicate forms while favouring the preservation of the larger and more robust ones, resulting in an orictocoenosis only partially representing the original assemblage (Fig. 1).
To extract the (paleo)ecological signal from the fossil record, in order to make ecological and subsequent oceanographic inferences, the effects of advection and reworking, variations in sedimentation and diagenesis must be quantified and removed.
Distortions induced by diagenesis can be significantly reduced by: (1) studying late Holocene sediment records for which diagenesis can be assumed to be negligible, and/or (2) selecting species with a similar degree of resistance to dissolution/recrystallization. The removal of such effects results in taphocoenoses that are now only affected by biostratonomical advection, sediment reworking and variations on sediment accumulation rate. To remove the latter effects in order to access the thanatocoenosis' (paleo)ecological signal, determining the coccolith (or nannolith s.l.) fluxes (nanno/cm2/year) from a constant sedimentation rate may be a solution. However, current radiometric methods commonly used for determining sediment accumulation rates in continental margin settings provide only averages over decadal to centennial time periods, thus lack the desired finer resolution. In addition, effects of bioturbation can often not be accounted for in the calculation of sediment accumulation rate, leading to considerable errors especially in slowly-accumulating sediments from open continental slopes (see Carpenter et al., 1982, Fuller et al., 1999, Boer et al., 2006). Finally, in regions of high sediment accumulation rates such as submarine canyons (De Stigter et al., 2007, De Stigter et al., 2011) coccolith fluxes derived from present day productivity are likely to end up mixed with resuspended/reworked coccoliths, due to the fact that these major submarine valleys often act as morphological depocentres of fine particles in transit along the shelf.
Determining species percentages relative to the sum of total (or selected) common coccoliths are a standard analytical procedure to eliminate the effect of the (common) taphonomical factors that indiscriminately act upon the biocoenoses, thus allowing to infer the species ecological inter-relationships independent of the effects from sediment dilution and/or bottom dynamics. Such factors are, thus, assumed to affect all coccolithophore species of similar size (≥ 3 μm) equally. Yet, given that coccolith assemblages fall into the category of compositional data, they are affected by spurious correlations and subcompositional incoherence, for which percentage determinations often lead to partial loss and/or misunderstanding of part of the information within compositional natural systems (Pawlowsky-Glahn and Egozcue, 2001, Buccianti, 2013). Even if one applies the strategies mentioned above, the interplay of all these environmental factors is likely to induce subcompositional incoherence if non-log ratio methods are used to investigate compositional data.
Compositional data can be defined as any data in which the components represent “parts of a whole”. They carry only relative information between parts, and are usually represented as percentages, in which case, their sum corresponds to a constant, typically 100% (Parent et al., 2012). Because of this, compositional data are an easy target of spurious correlations and subcompositional incoherence that typically affect any data measuring parts of the same whole. An example: considering an ecological subsystem composed of a few selected species (sp1, sp2, sp3, … spn), the behaviour of any two components will randomly change their signs (i.e., if they are positively or negatively correlated) and meanings depending on the other components involved (Pearson, 1897, Tolosana-Delgado, 2012, Buccianti, 2013). Ideally, if the above mentioned strategies (1) and (2) have been applied, results should not depend on whether we take a few, several, or all of our components or species, neither on whether we scale them up and down by arbitrary numbers, nor even whether we choose our samples to sum up to 100% or leave them untouched (Aitchison, 1997). But due to the properties of compositional data, the results obtained from their percentages may in fact vary significantly.
To avoid these problems, and to ensure that all the available information is being extracted from the data, two fundamental properties should be inherent to the methods applied when studying compositional data: “scale invariance” and “subcompositional coherence”. This means that whether one represents the data in percent, ppm or some other unit, and whether one closes the analysis for two, three or ten species, the results, i.e., the relationships between the species, will be the same and coherent among themselves.
Compositional Data Analysis (CoDA), based on the idea that we can only assess relative changes between components, provides a set of statistical tools and geometric concepts built with the purpose of allowing results to satisfy scale invariance and subcompositional coherence (Aitchison, 1997). By avoiding spurious correlations and negative bias, the log-ratio approach allows obtaining an understanding on how natural phenomena work while extracting all the information contained in data variability (Buccianti, 2013). Although similar results may be achieved from both classical and compositional approaches, depending on which are the typical values of the percentages and their spread, it is not possible up to now to know the weight of this effect a priori, or even to measure it (see Pawlowsky-Glahn and Egozcue, 2001, Tolosana-Delgado, 2012).
In our study, CoDA is used to study the (paleo)ecology of coccolithophores from the central Portuguese margin. The isometric log-ratio (ilr) approach (e.g., Egozcue et al., 2003, Egozcue and Pawlowsky-Glahn, 2005, Thió-Henestrosa et al., 2008, Tolosana-Delgado, 2012) was applied to (1) validate (paleo)ecological trends previously inferred from the species percentages (Guerreiro et al., 2015), (2) confirm the potential of coccoliths as proxies of environmental phenomena intensified in submarine canyons, and (3) introduce CoDA as a method to validate and obtain consistent (paleo)ecological interpretations. Results obtained from CoDA are compared with results from classical approaches (i.e., coccolith concentrations, species relative percentages and coccolith fluxes) and are further discussed.
Section snippets
Regional setting
The central Portuguese margin has a relatively narrow shelf (20–50 km wide and a gradient of < 1°), passing into a steep irregular slope (6–7°) below the shelf-break which is located at 160–200 m depth (Fig. 2). The shelf is composed of thick Cenozoic carbonate and detritic formations, filling structural basins formed during earlier rifting phases. The margin is dissected by a number of long submarine canyons, of which the Nazaré and Setúbal–Lisbon Canyons are the most significant (e.g., Vanney
Cruises and surface sediment sampling
The sediment samples used in this study were collected during several cruises with RV Pelagia of Royal NIOZ, held in November 2002, October 2003, April/May 2004, May 2005, September 2006 and March 2011 in the central Portuguese margin (cruises 64PE204, 64PE218, 64PE225, 64PE236, 64PE252 and 64PE332, respectively).
A total of 87 surface samples from depths between 48 and 4987 m were collected with equipment and methodology as described in De Stigter et al., 2007, De Stigter et al., 2011. Samples
CoDA: Isometric log-ratios (ilr)
The dendrogram (see Pawlowsky-Glahn and Egozcue, 2011) represented in Fig. 3 gives information about the relative importance of each (paleo)ecological assemblage (oceanic vs. coastal-neritic) within the five investigated sectors. Each balance (β) is represented by a black vertical bar, the length of which is proportional to the variance explained by the balance, considering the whole set of samples (i.e., as one unique sample).
Each sector (assumed to be well represented by a group of samples)
(Paleo)ecology of coccolithophores based on isometric log-ratios
Results presented in this study are in good agreement with distribution trends recently reported by Guerreiro et al. (2015) for this dataset, using the percentages (Section 4.1): distinct (paleo)ecological N–S and W–E trends were observed between the seven taxonomic groups, and differences were also observed between the submarine canyons and the adjacent shelf and slope regions. Such ecological trends were also earlier obtained by Guerreiro et al. (2011), using the centred log-ratio approach
Conclusions
Despite of potentially spurious correlations and biased statistical analysis associated with classical methods, results obtained with isometric log-ratio coordinates are in good agreement with results previously obtained from the species percentages. While avoiding the major statistical problems of dealing with percentages and ensuring the preservation of sub-compositional coherence within the data set, CoDA allowed to validate the existence of a coastal-neritic (H. carteri, G. oceanica and C.
Acknowledgements
Data for this study were collected in the framework of the EU-funded EUROSTRATAFORM (contract EVK3-CT-2002-00079) and HERMES EU-funded projects (contract GOCE-CT-2005-511234), ‘‘Lead in Canyons’’ and “Pacemaker” projects funded by the Netherlands Organization for Scientific Research, and by the Portuguese project Cd Tox-CoN (FCTPTDC/MAR/102800/2008). Multicores were collected during RV Pelagia cruises which were funded by the Netherlands Organisation for Scientific Research. Samples were
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