DOI: 10.5061/dryad.5dv41ns65
title: Systematics and conservation of an endemic radiation of Accipiter hawks in the Caribbean islands

description: More than one third of the bird species found in the Caribbean are endemic
 to a set of neighboring islands or a single island. However, we have
 little knowledge of the evolutionary history of the Caribbean avifauna and
 the lack of phylogenetic studies limits our understanding of the extent of
 endemism in the region. The Sharp-shinned Hawk (Accipiter striatus) occurs
 widely across the Americas and includes three endemic Caribbean taxa:
 venator on Puerto Rico, striatus on Hispaniola, and fringilloides on Cuba.
 These island populations have undergone extreme declines presumably due to
 ecosystem changes caused by anthropogenic factors, as well as due to
 severe hurricanes. Sharp-shinned Hawks in general, and Caribbean
 Sharp-shinned Hawks in particular, have not been placed in a modern
 phylogenetic context. However, the island taxa have historically been
 presumed to have some ongoing gene flow with mainland populations. Here we
 sequenced ultraconserved elements (UCEs) from 38 samples, focusing on
 Caribbean taxa. Using a combination of UCEs and thier flanking regions,
 mitochondrial genome sequences, and single-nucleotide polymorphisms
 (SNPs), we investigated the phylogenetic relationships among Caribbean
 lineages and their relationships to mainland taxa. We found that Caribbean
 Sharp-shinned Hawks are reciprocally monophyletic in all data sets with
 regard to mainland populations and among island taxa (with no shared mtDNA
 haplotypes) and that divergence in the NADH dehydrogenase 2 gene (ND2)
 between these mainland and island groups averaged 1.83%. Furthermore, sNMF
 analysis indicated that Hispaniola, Puerto Rico, and mainland samples each
 form separate populations with very limited admixture. We argue that our
 findings are consistent with the recognition of the three resident
 Caribbean populations as species-level taxa, because both nuclear and
 mitochondrial genetic data indicate reciprocal monophyly and have
 species-level divergences there is no sharing of mitochondrial haplotypes
 among or between island taxa and those on the mainland; and they are
 diagnosable by plumage.
description: For full methods see the associated paper, but briefly- libraries
 were enriched for UCEs using either the 2.5k tetrapod probe kit (2,386
 UCEs) supplemented with approximately 100 avian exons, or the standard 5k
 tetrapod probe kit (5,060 UCEs; Faircloth et al. 2012). Libraries were
 sequenced with either 100 bp (2.5k kit) or 150 bp (5k kit) paired end
 reads on an Illumina HiSeq 3000/4000.  After duplicate removal and quality
 trimming we assembled UCEs using aTRAM v. 2.3.0 (Allen et al. 2018) and
 the longest contig for each sample was aligned in MAFFT (Katoh 2013). 
 Each alignment was verified by eye using Geneious 8.0.4 (https://www.geneious.com). To address sequencing error associated with degraded DNA extracted from toepads we first removed unalignable portions of a contig.  Next, we then looked for individual mismatches within each alignment. In the case of tissue or blood samples, if mismatches occurred towards the center of a sequence (outside of the 15 bases on either end), these mismatches were kept. However, for toepad samples, we re-coded mismatches as “N” regardless of where in the sequence the mismatch occurred because coverage was lower across the entire sequence, whereas tissue and blood samples had low coverage typically only at the ends. When a mismatch was identical to any other sequence, regardless of whether the sequence it matched was extracted from frozen tissue, blood, or a toepad, we retained the base call.