DOI: 10.5061/dryad.q83bk3jtf
title: Data from: Different traits dominate evolution at early and late stages of adaptive radiation

description: Adaptive radiation (AR), a process of rapid speciation and
 ecomorphological diversification, played an important role in generating
 past and contemporary global biodiversity. An unsolved question is what
 maintains high rates of speciation during AR, a phenomenon we call
 “speciation paradox”. One possible explanation for resolving this paradox
 is a sequential trait evolution, i.e., a series of ecological
 diversifications, which enables evolving lineages to fully and more
 effectively exploit the ecological space. We tested this hypothesis using
 the highly diverse subterranean amphipod genus Niphargus. Niphargus shows
 distinct signatures of adaptive radiation both at the genus level and at
 the level of four larger clades. Our analysis revealed decoupled evolution
 of habitat-related traits and trophic-biology-related traits. Moreover, on
 a genus level, we found the evidence that AR commences with a tight
 association between speciation rates and the dynamics of habitat-related
 traits. At a later stage, speciation dynamics become associated with
 diversification of trophic-biology-related traits. This suggests that the
 dependence of macroevolutionary rates in this group switches
 among niche axes before saturation, resulting in prolonged high speciation
 rates during AR.
description: We assembled an extensive dataset on species phylogeny, ecology,
 and functional morphological traits across the adaptive radiation
 of <em>Niphargus</em>. We used the molecular taxonomic units
 (MOTUs) and phylogeny produced in Delić et al. (2025), and morphological
 and ecological data of analysed species, produced in Premate et al.
 (2024). The analyses consist of three parts: decoupled
 diversification, states-dependent speciation and extinction, and
 speciation rate modelling. All analyses were first conducted across the
 entire genus. Next, we looked for independent replicates of
 diversification within the entire AR. We selected four large monophyletic
 clades with diversification patterns consistent with AR predictions (Borko
 et al., 2021). 1) DECOUPLED DIVERSIFICATION
 To test whether diversification bursts of the functional trait
 classes differ in time, we analyzed the dynamics of trait space filling
 through time for each functional trait class separately (i.e., traits
 associated with habitat (namely habitatPC1 and habitatPC2) and traits
 linked to feeding abilities (namely trophicP and trophicD)). For each
 trait class separately, we first reconstructed ancestral states using the
 best model of trait evolution, using R packages phytools (Revell, 2024)
 and mvMORPH (Clavel et al., 2015). Next, we used the best model of trait
 evolution to reconstruct ancestral states of traits (Clavel et al., 2015).
 We analysed the course of evolution for each functional trait class by
 reconstruction of morphospace expansion through time, following the
 procedure of Ronco et al. (2021). 2) STATES-DEPENDENT
 SPECIATION AND EXTINCTION We fitted maximum likelihood
 SSE models (State-dependent Speciation and Extinction; Maddisson et al.,
 2007, Herrera-Alsina et al., 2019) where per-lineage speciation rates
 depended on the particular state of a given trait (i.e., traits associated
 with habitat (namely habitatPC1 and habitatPC2) and traits linked to
 feeding abilities (namely trophicP and trophicD)). We modelled trait-class
 dynamics as the change from one state to another over time.
 3) SPECIATION RATE MODELLING<br>To model speciation rates
 through time, we used birth-death diffusion (BDD) models, using Julia
 package <em>Tapestree</em> (Quintero et al., 2024).
description: # Different traits dominate evolution at early and late stages of adaptive
 radiation Code.zip contains all R scripts and data needed for analyses in
 the paper. It is divided in three parts, DECOUPLED DIVERSIFICATION (folder
 1), STATES-DEPENDENT SPECIATION AND EXTINCTION (folder 2), AND SPECIATION
 RATE MODELLING (folder 3). ## 1) DECOUPLED DIVERSIFICATION **data** folder
 contains phyogeny, morpho and eco data, species by clades, and RDS with
 imputed values for missing traits. Specifically, it contains the files: *
 **20221213_niphargus.tree**: phylogeny of Niphargus * **clades.csv**: MOTU
 labels used in phylogeny, with their respective subclade, for four
 analysed subclades. MOTUs outside of four clades are treated as
 "backgroud phylogeny" and have no label. * **ecology.xlsx**:
 ecology of each MOTU (categorical variable) *
 **Groundwater_Amphipoda_functional_trait_database_V1_extended.xlsx**:
 functional trait database, see Premate et al. 2024 for details *
 **morphology_imputed.rds**: R data file with imputed values for missing
 functional trait data * **speciesA1.txt**: MOTUs in subclade A1
 (Pannonian) * **speciesA2.txt**: MOTUs in subclade A2 (Pontic) *
 **speciesB.txt**: MOTUs in subclade B (South Dinaric) * **speciesC.tx**t:
 MOTUs in subclade C (West Balkan) **Niphargus_trait_evolution.rmd** file
 runs neccessary packages and scripts and outputs results. Note that
 working directory and "result" folder need to be defined before
 you run the script. **00_data.R**: import and data manipulation, including
 imputation of missing values to morpho ds. All variables needed in later
 analyses are defined here, including subsets, subclades, etc.
 **00_functions.R**: all custom functions **01_figure1_phylogeny.R**: plots
 half-circle phylogeny **02_regression_PCA.R**: runs phylogenetic
 regression and PCA, and saves results **03_kmeans.R**: calculates k-means
 and saves results **04_modeling.R**: runs modeling, ancestral trait
 reconstruction and morphospace expansion through time, simulations and
 comparison of morphospace expansion of real and simulated data. ## 2)
 STATES-DEPENDENT SPECIATION AND EXTINCTION This folder includes data and
 code used for sec_sse analysis. The analysis was run on whole genus and
 three major clades. Additionally, trophic trait classes were compared with
 habitat trait class (trophicD and trophicP), so overall, 8 combinations of
 model comparisons were performed. The folder is thus divided into
 "clades" and "whole_genus" subfolders. Data and R
 scripts for model setup (**01_model_setup.R**), launching the analysis
 (**02_launch_analysis.R**) and calculation of AIC values
 (**03_clades_aic_depths.R**) are provided. **data** folder contains
 phyogeny (same as above), species by clades (same as above), and
 transformed continuous morphological traits into categorical (k-means) for
 each MOTU (k-means are in summary files named **kmeans_cladeX.csv**, and
 in files formatted for analysis, named **cladeX_traitX.csv**). K-means
 were calculated
 from **Groundwater_Amphipoda_functional_trait_database_V1_extended.xlsx**
 dataset, for four trait classes: habitat PC1, habitatPC2, trophicP and
 trophicD. See scripts under 1) for details. ## 3) SPECIATION RATE
 MODELLING This folder includes Julia script **speciation_rate.jl** and
 data, used for modelling speciation rates through time (birth-death
 diffusion models), using package Tapestree. Data includes phylogeny in
 newick format (**20221213_niphargus_newick.tre**) and sampling
 completeness file with % of completeness for each species in the tree
 (**niphargus_rho1.csv**).