DOI: 10.5061/dryad.sn02v6xdm
title: Past environmental change and seasonal migration shaped pronounced variability in the phylogenomic history of a morphologically cryptic bird radiation

description: Aim: Demographic inferences in combination with phylogenomic
 reconstructions provides a promising avenue to better understand the
 impact of past environmental changes on biogeographic patterns, yet we
 have only begun to exploit this potential. Here, based on genome
 resequencing data, we studied how regionally contrasting environmental
 conditions and variation in seasonal migration behaviour and dispersal
 ability influenced diversification of a cryptic bird radiation containing
 evolutionary lineages with extensive variation in distribution ranges
 across Eurasia. Location: Eurasia Taxon: Avian genus Riparia
 Methods: We analyzed full genome data of 24 individuals, including all
 Eurasian Riparia taxa, using multi-pronged phylogenomic and demographic
 analyses. Hand-wing index (HWI) was used as proxy for migration and
 dispersal behaviour. Results: Collared R. riparia and pale sand
 martin R. diluta showed genomic divergence at inter- and intraspecific
 level, aligning with described subspecies. The large Eurasian range of
 nominate R. r. riparia resulted from prolonged population growth during
 the Late Pleistocene rather than recent post-glacial expansion as
 suggested earlier from mitochondrial DNA. Pronounced seasonal migration
 and dispersal propensity likely allowed the colonization of a large range
 and impeded population differentiation. However, the divergence of
 southern R. r. shelleyi likely happened through a reduction in seasonal
 migration behaviour. The four evolutionary lineages of R. diluta showed
 independent demographic trajectories. After initial differentiation in
 contrasting environments, evolution of distinct seasonal migration
 behaviour likely became crucial for maintaining genomic diversity.
 Conclusions: Our comparative genomic analyses allowed us to pinpoint how
 regional variation in past environmental changes and life-history traits
 led to contrasting evolutionary trajectories in a single bird radiation.
 This underpins the importance of such analyses across the tree of life to
 increase our understanding of the factors shaping species’ demographic
 histories, not at least for assessing their potential reaction to current
 human-induced climate change.
description: We analyzed full genome data of 24 individuals including all
 Eurasian <em>Riparia</em> taxa using multi-pronged
 phylogenomic and demographic analyses. Hand-wing index (HWI) was used as
 proxy for migration and dispersal behaviour.
description: # Past environmental change and seasonal migration shaped pronounced
 variability in the phylogenomic history of a morphologically cryptic bird
 radiation DOI: 10.5061/dryad.sn02v6xdm This data file contains a sample
 list with more detailed information
 (Sample_list_Riparia_phylogeny_detailed.xlsx) and datasets for different
 analysis: Description of variables in the sample list: Sample ID and
 Locality Id used in the paper, Locality, Coordinates and Collecting dates
 are information of where and when the sample were collected, Tissue: Type
 of tissue sampled for resequencing, SRA and BioSample ID are the ID
 information for the raw fastq files of each individual stored in NCBI.
 Format of dates:day/month/year. NA for data not available.  fasta
 alignments of 45810 unlinked windows and the total number of 91620 windows
 for the species tree analysis: *
 Riparia_fasta_45810windows_compressed.tar.gz *
 Riparia_fasta_91620windows_compressed.tar.gz fasta alignments of 8
 mitochondrial protein-coding genes: * Riparia_Mitochondrial_alignments.zip
 vcf of called SNPs, including invariable sites, removing indels and
 repeats: * holo_25_recall_indel_repeats_removed.vcf.gz vcf files for
 Dsuite analysis: * Riparia_Dsuite.vcf.gz bam files for psmc analysis: *
 Riparia_psmc_bam_1.tar.gz * Riparia_psmc_bam_2.tar.gz *
 Riparia_psmc_bam_3.tar.gz The Sequence ID in each file corresponds to the
 Sample ID in the paper as follows: | Sequence ID | Sample ID | | :- | :- |
 | H5 | NHMUK1920.10.24.1 | | H2 | NHMUK1949.WHI.5879 | | RdfMx6531 |
 SYSb006531 | | Rdfyb10 | SYSb008379 | | RdfWz3792 | SYSb003792 | | RdtRm44
 | SYSb004194 | | RdtZg02 | SYSb003656 | | RdtLs20 | SYSb004154 | | RddWjq
 6542 | SYSb006542 | | RddAla102 | SYSb006522 | | RddKho116 | SYSb007338 |
 | RrrZz6508 | SYSb006508 | | RrrM27 | NMBE1078313 | | RrIsr2 | El2 | |
 RrIsr3 | El3 | | RrsIsr12 | El12 | | RrrBsm168 | SYSb008357 | |
 RrrEur136392 | ZMUC136392 | | RrrEur137192 | ZMUC137192 | | RrrEur116734 |
 ZMUC116734 | | Rp132634 | ZMUC132634 | | A6 | NHMUK1965.M.8237 | | G5 |
 NRM-U-663 | | F5 | NRM-U-664 |