DOI: 10.5061/dryad.stqjq2c3x
title: Major population splits coincide with episodes of rapid climate change in a forest-dependent bird

description: Climate change influences population demography by altering patterns of
 gene flow and reproductive isolation. Direct mutation rates offer the
 possibility for accurate dating on the within-species level but are
 currently only available for a handful of vertebrate species. Here, we use
 the first directly estimated mutation rate in birds to study the
 evolutionary history of pied flycatchers (Ficedula hypoleuca). Using a
 combination of demographic inference and environmental niche modelling, we
 show that all major population splits in this forest-dependent system
 occurred during periods of increased climate instability and rapid global
 temperature change. We show that the divergent Spanish subspecies
 originated during the Eemian-Weichselian transition 115 – 104 thousand
 years ago (kya), and not during the last glacial maximum (26.5 - 19 kya),
 as previously suggested. The magnitude and rates of climate change during
 the glacial-interglacial transitions that preceded population splits in
 pied flycatchers were similar to, or exceeded, those predicted to occur in
 the course of the current, human-induced climate crisis. As such, our
 results provide a timely reminder of the strong impact that episodes of
 climate instability and rapid temperature changes can have on species’
 evolutionary trajectories, with important implications for the natural
 world in the Anthropocene.
description: Species distribution modeling. We used the ensemble approach
 implemented in the R package biomod2 to model the breeding distribution of
 pied flycatchers for the past 200,000 years using paleoclimate data
 published in Beyer et al. 2020 (<em>Scientific Data</em>).
 Each of the four chosen climate variables (minimum temperature,
 temperature variability, minimum precipitation, precipitation variability)
 represent averages across the breeding season (May, June, and July). Pied
 flycatcher occurrence data consist of breeding evidence records from the
 European Breeding Bird Atlas 2 (EBBA2) project for Europe, and of gbif
 occurrence data for the region east of the Ural mountains.
 Demographic modeling: We used DADI (Gutenkunst et al. 2010,
 <i>Nat Prec</i>) to fit a model of ancestral size change,
 followed by a split-with-migration, to two-dimensional site frequency
 spectra of pied flycatchers. This model was previously found to provide
 the best fit to pied flycatcher genetic data (Warmuth & Ellegren,
 2019, <em>Mol Ecol Res</em>). Site frequency spectra were
 derived from ddRADSeq data and generated using ANGSD. The populations
 represent a subset of populations in Lehtonen et al 2009 (<em>Mol
 Ecol</em>). For further details, please refer to
 the publication associated with this entry.
description: Occurrence data (file: sdmdata.csv) are a combination of the
 EBBA2 breeding evidence dataset (50x50km) and gbif data for the region
 east of the Ural mountains (not covered by the EBBA2 dataset). Gbif
 occurrence data were filtered to include only occurences from the months
 of may, june and july. The combined dataset (EBBA2 and gbif) was filtered
 for duplicates and represents one occurrence point per grid cell
 (50x50km). Genetic data (folder: bam_files). Fastq
 files were mapped to a version of the <em>Ficedula
 hypoleuca</em> reference genome that no longer exists in the public
 domain. We have therefore included the mapped reads (bam files) rather
 than the raw fastq files. For details on the mapping parameters, see
 Warmuth & Ellegren, 2019, <em>Mol Ecol
 Res</em>.