Long-term changes and geographic convergence of southeastern Pacific intertidal communities
Creators: name: Orostica, Mauricio
name: Arancibia, Paulina
name: Ovaskainen, Otso
name: Navarrete, Sergio Andres
name: Broitman, Bernardo
Publisher: name: Zenodo
Year: 2025

description: Abstract: Understanding how multispecies assemblages jointly respond to environmental fluctuations is one of the main challenges for modern ecology. Most studies, however, have examined coexistence mechanisms within phylogenetically or taxonomically homogenous groups, thus limiting our understanding of mechanism of coexistence under environmental change. This study rests on 23 years of systematic quantitative ecological surveys across nine degrees of latitude along the central-southern Humboldt upwelling ecosystem, to assess how multispecies assemblages have, or have not, responded to climatic variability. Using satellite sea surface temperature (SST) statistics as an integrative proxy of environmental variability, we assessed to what extent the phylogenetic baggage and species traits help us understand community changes over time and space. We hypothesized that the long-term responses to environmental variability, of communities that are locally modulated by strong species interactions, can be decomposed into functional subsets based on traits and taxonomy. Employing joint species distribution models (Hierarchical Modelling of Species Communities), which combine taxonomy with a suite of biological traits, we aimed to disentangle spatial and temporal shifts in the composition of intertidal zone communities. We found that taxonomic classification and species traits were weakly associated with species responses to SST variability patterns. However, we identified a consistent increase in the occurrence of macroalgal and invertebrate species across the region. No species decreased their occurrence over time. The occurrence of macroalgal species was more sensitive to mean SST than invertebrates, and their responses shifted from positive in the equatorward to negative in the poleward sites. Larger macroalgae were negatively affected by changes in mean SST, and patterns of co-occurrence of macroalgal and invertebrate species were strongly dependent on spatial scale. Thus, our findings indicated that, unexpectedly, multispecies responses were not affected by their phylogenetic baggage, demonstrating that taxonomic structure was not informative, and species traits were of moderate use to understand environmental long-term responses. Moreover, our results suggest a lack of community-wide changes and highlight the broader implications of environmental forcing as a driver of biodiversity patterns, which may be modulated by the regional cooling driven by the intensification of coastal upwelling.
description: README

This repository includes: 

Six R scripts for setting up, fitting and postprocessing the HMSC analyses for intertidal species. These scripts must be executed in the specified order, i.e., S1, S2, S3, S4, S5, and S6. These files encompass data from 22 field sites surveyed between 2000 and 2023 across nine degrees of latitude along the Chilean coast.

The essential data for HMSC analyses include (see Ovaskainen & Abrego 2020 for details):

1) Matrices of intertidal species occurrences of macroalgae and invertebrates (Y_algae and Y_invr, respectively)

2) A matrix of environmental covariates (X_Data).

3) Macroalgal and invertebrate traits (TrData_algae and TrData_invr, respectively).

4) Phylogenetic-taxonomic relationships (my.taxonomy_algae and my.taxonomy_invr, respectively).

5) Spatiotemporal sampling design (studyDesign).

Ensure that your working directory includes the following folders: data, models, and results. Save the raw data file (`raw_data_oros_etal25`) in the "data" folder.

Required R packages (additional packages may be required, as detailed in individual scripts):

install.packages("ape")install.packages("Hmsc")

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There are eight data.frames contained in "raw_data_oros_etal25":

First and second: "my.taxonomy_algae" and "my.taxonomy_invr".

Descriptions: each file contains a table with 6 columns.

"kingdom""phylum""family""genus""species"

Third: "studyDesign".

Description: the file contains a table with 3 columns.

"site""bench""year"

Fourth and Fifth: "TrData_algae" and "TrData_invr".

Descriptions: each file contains a table with 3 and 4 columns, respectively.

"life_cycle""max_length""lifespan"

"tiering""feeding""larva""max_size"

Sixth: "XData".

Description: the file contains a table with 4 columns.

"year""height""ann_anom""ann_mean"Seventh and eighth: "Y_algae" and "Y_invr".

Description: species abundance matrices with 47 spp (Y_algae) and 51 spp (Y_invr), respectively.