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Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock

Citation

Thacker, Christine et al. (2022), Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock, Dryad, Dataset, https://doi.org/10.5061/dryad.xd2547ddw

Abstract

Adaptive radiations are generally thought to occur soon after a lineage invades a region offering high levels of ecological opportunity. However, few adaptive radiations beyond a handful of exceptional examples are known, so a comprehensive understanding of their dynamics is still lacking. Here, we present a novel case of an island species flock of freshwater fishes with a radically different tempo of adaptive history than that found in many popular evolutionary model systems. Using a phylogenomic dataset combined with simultaneous Bayesian estimation of divergence times and trait-based speciation and extinction models, we show that the New Zealand Gobiomorphus gudgeons comprise a monophyletic assemblage, but surprisingly, the radiation did not fully occupy freshwater habitats and explosively speciate until more than ten million years after the lineage invaded the islands. This shift in speciation rate was not accompanied by an acceleration in the rate of morphological evolution in the freshwater crown clade relative to the other species, but is correlated with a reduction in head pores and scales as well as an increase in egg size. Our results challenge the notion that clades always rapidly exploit ecological opportunities in the absence of competing lineages. Instead, we demonstrate that adaptive radiation can experience a slow start before undergoing accelerated diversification and that lineage and phenotypic diversification may be uncoupled in young radiations.

Methods

Methods are described in the publication, with additional details in the deposited file Gobiomorphussupplementalmethods.docx.

UCE raw reads are available under NCBI BioProjects PRJNA348720 (Mogurnda adspersa) and PRJNA659476 (all other samples).

Usage Notes

Supplemental Figures and Tables are identified by number (S1-S3 and T1-T4)

Gobiomorphus1_1000_95p.phylip and Gobiomorphus1_1000_75p.phylip are the 95% and 75% taxon complete UCE alignments, and Gobiomorphus1_1000_75p.charsets and Gobiomorphus1_1000_95p.charsets are the files listing partitions for each UCE locus

InstructionsforRevBayes.txt details how to prepare datafiles and run the RevBayes analysis (gobiomorphustreePLconfig is used in preparing the ultrametric tree).

RevBayesfiles.tar contains the scripts and datafiles for running the RevBayes analyses.

gobiomorphusdata.xls is the spreadsheet of morphometric measurements for Gobiomorphus species, including ln transformed values

Gobiomorphussupplementalmethods.docx is the methods supplement, describing details of UCE sequencing and alignment and phylogenetic analyses

Funding

Ministry of Business, Innovation and Employment

Waikato Regional Council