DOI: 10.5061/dryad.73n5tb2x6
title: Genomic data reveal the biogeographic and demographic history of Ammospiza sparrows in northeast tidal marshes

description: Aim: Shaped by both climate change and sea-level rise, tidal salt marshes
 represent ephemeral systems that are home to only a few, highly
 specialized species. The dynamic ecological histories and spatial
 complexities of these habitats, however, render it challenging to
 reconstruct the complete biogeographic histories of their endemic taxa.
 Here, we leverage three species of North American Ammospiza sparrows that
 inhabit tidal marshes ( Ammospiza caudacuta, A. maritima, and A. n.
 subvirgatus) and closely related freshwater species to demonstrate the
 utility of whole-genome data in resolving demographic and evolutionary
 history as it relates to divergence and dispersal events in ephemeral
 ecosystems. We employ a combination of demographic and biogeographic
 reconstructions to shed new light on the colonization history of
 freshwater-saline environments in this system. Location: North America
 Taxon: Ammospiza Sparrows Methods: We sequenced whole genomes from
 Ammospiza sparrows to address our objectives. We conducted phylogenomic
 analyses and reconstructed the demographic and biogeographic history of
 this clade based on 21 million SNPs from 54 total individuals. Results:
 Phylogenies based on several million SNPs supported several well-resolved
 clades that predominantly corresponded to their prior species
 designations. Phylogenetic and biogeographic reconstructions suggest a
 series of saltwater to freshwater colonization events within this group,
 with some endemic taxa exhibiting associations with tidal marsh habitat
 over longer evolutionary time scales and some habitat transitions
 occurring as recently as 5,000 years ago.  Main Conclusions: Our
 reconstructions support a biogeographic hypothesis with fewer vicariance
 and dispersal events among Ammospiza sparrows that is in contrast with the
 currently supported evolutionary scenario. Biogeographic reconstructions
 further suggest saltwater to freshwater transitions in A. n. subvirgatus
 as opposed to the long hypothesized freshwater origin. Our results
 highlight the fact that reconstructing biogeographic and evolutionary
 dynamics in ephemeral systems poses challenges given the propensity for
 high turnover. This reinforces the importance of a multifaceted approach
 to biogeographic reconstructions in historically dynamic ecosystems.
description: We prepared individually indexed libraries using 1 µg of DNA following the TruSeq DNA PCR free library preparation kit protocol (San Diego, CA, USA), with an insert size of 350 bp. We pooled 24 libraries using concentrations of adapter-ligated DNA determined through digital PCR. The pooled libraries were sequenced on three Illumina NextSeq500 lanes at the Cornell Institute for Biotechnology core facility. Each lane contained 24 individuals, as some samples were run with samples for a different study. The quality of individual libraries was assessed using FastQC (version 0.11.5; http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads were aligned to the <i>A. caudacuta </i>reference genome (Walsh et al. 2019a). We performed sequence trimming, adapter removal, and quality filtering with AdapterRemoval version 2.1.1 (Lindgreen 2012). We allowed a minimum threshold quality score of 10 (increased from the default value of 2) and merged overlapping paired-end reads. Filtered reads were aligned to the reference using bwa 0.7.4 (Li and Durbin 2009) with default settings. Alignment statistics were obtained using qualimap version 2.1.1 (Okonechnikov et al. 2015).              BAM files were sorted and indexed using SAMtools version 1.3 (Li et al. 2009). We realigned around indels and fixed mate-pairs using GATK version 3.5 (McKenna et al. 2010). SNP variant discovery and genotyping for the 54 individuals was performed using BCFTools (-mpileup and -call). For an initial filtering step, variants that were out of Hardy-Weinberg equilibrium, had a minor allele frequency less than 2%, had a mean depth less than 2 or greater than 50, and more than 20% missing data were filtered from the data set using VCFtools version 0.1.14 (Danecek et al. 2011). This initial filtering step resulted in 21,622,990 SNPs. 
description: Individuals are named by species abbreviation and a
 number. LCSP: A. leconteii Nelsoni:
 A. n. nelsoni SALS: A. caudacuta