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Niche conservation in copepods between ocean basins

Citation

McGinty, Niall et al. (2021), Niche conservation in copepods between ocean basins, Dryad, Dataset, https://doi.org/10.5061/dryad.8931zcrrf

Abstract

This dataset provides the necessary data to test for niche conservatism as demonstrated in the article "Niche conservatism in copepods between ocean basins; 10.1111/ecog.05690". 

Our study examined niche conservatism (i.e. a species' niche remains stable in space and time) between populations of the same species of marine copepod in different ocean basins. We used two approaches to test for niche conservatism which can be defined as a Princpial Component Analysis (PCA) and Environmental Niche Model (ENM) method. Niches may differ by virtue of the fact that the available environmental conditions do not overlap. This can be addressed by first establishing a baseline or a null model that quantifies how far a niche would be expected to differ by chance based on the environmental conditions in both areas. We used six environmental variables to define the environmental niche (sea surface temperature - SST °C, Salinity, mixed layer depth - MLD (m), bathymetric depth (m), chlorophyll-a - chl-a (mg m-3) and wind stress (N m-2).

The PCA method uses the first 3 principal components to define the species niche in each population and the available background conditions in each area. If the niche distance between two populations is found to be significantly LESS than the distance in mean background conditions then the niches are judged to be conserved even if they are different. In contrast, if the niche distances are significantly different and MORE than the distance in mean background conditions then the niches are judges to be diverged. 

The ENM method compares the niches of two populations by using Maximum Entropy modelling (MaxEnt) to first define each popultions distributions across the environmental gradients. The niche overlap between two different populations were quantified using the Schoener's D metric where 0 = no niche overlap to 1 = full niche overlap. To separate the effect of different background conditions on the level of niche overlap (D), a null distribution (H0) was generated for each population by
calculating the differences between 100 ENMs generated using the presence data of one population and random background samples from the other population. If  H0 < D, the niches overlap greater than would be expected purely by chance and are therefore conserved. In contrast If  H0 > D the niches overlap less than would be expected by chance and are therefore diverged.

Of the 21 pairwise comparisons between populations of the same species a total of 10 showed evidence of niche divergence. The divergent popaultions belonged to 7 of the 15 marine copepod species with the majority belonging to the genus Pleuromamma. The findings have important implicatons on the use of  ecological models in defining the niche of marine copepods as regional populations may respond differently to environmental pressures. Evidence of strong genetic variation has been shown for many of these species with the potential for adaptive evolutionary response to regional pressures at a much faster rate than expected. Given this fact we encourage future studies to incorporate phylogenetic information into niche model analyses for plankton.

Methods

Both biological and environmental data are freely available for download.

The copepod data were collected by the Continuous Plankton Recorder (CPR) and extracted from the Archive for Marine Species and Habitats Data (dassh.ac.uk). 

The environmental data were extracted as monthly climatologies from the World Ocean Atlas while the bathymetric depth were extracted from GEBCO’s current gridded bathymetric data set (2020).

Usage Notes

The readme files contains a description of the variables used in this work. The associated comma delimited files (.csv) provides the data for 1 of the species (Nannocalanus minor) to perform the PCA and ENM method used in this paper. An associated R script shows the procudure for the PCA method. 

For further details please see the original paper.

Funding

Simons Foundation, Award: 549935 Irwin/Dal