DOI: 10.5061/dryad.xksn02vrh
title: Data from: What is an eared nightjar? Ultraconserved elements clarify the evolutionary relationships of Eurostopodus and Lyncornis nightjars (Aves: Caprimulgidae)

description: Nightjars (Aves: Caprimulgidae) are a species-rich family of birds, with
 the “eared nightjars” (Eurostopodinae) being an early-branching group
 endemic to the Indo-Pacific. While much research has focused on
 species-rich nightjar genera and their higher-level relationships, the
 evolutionary history of Eurostopodinae (Eurostopodus, Lyncornis) remains
 understudied. We generated a genome-scale dataset to produce the first
 fully sampled phylogeny of all Eurostopodus and one Lyncornis species,
 including sequencing two type specimens of critically endangered and
 extinct species. Tree-building methods inferred concordant, well-resolved
 topologies that reveal intriguing biogeographic patterns within
 Eurostopodus. Our results show Eurostopodus as sister to all other
 nightjars, while Lyncornis, previously considered related, is more closely
 allied with other caprimulgids. We propose that the term "eared
 nightjars" should apply only to the two Lyncornis species, which
 should be classified within the subfamily Caprimulginae. Accordingly,
 since only Eurostopodus species remain in Eurostopodinae, we recommend
 renaming this subfamily "Indo-Pacific nightjars" to reflect
 their geographic distribution in this significant region.
description: The goal of this study is to assess the evolutionary history of
 this understudied group of nightjars using a genome-scale dataset. We
 sampled all <em>Eurostopodus</em> species, including three
 species that have never been part of a molecular analysis before—two of
 which (<em>E. exul </em> and <em>E.
 diabolicus</em>) were sourced from toepad clippings of type
 specimens housed at the American Museum of Natural History.
 We collected a comprehensive genome-scale dataset of
 ultraconserved elements (UCEs), utilizing an updated probe
 set specifically refined to better capture UCEs from degraded,
 toepad-sourced samples. For wider taxonomic sampling, we downloaded whole
 genomes from GenBank to harvest UCE data <em>in silico</em>.
 We used both maximum likelihood and species tree methods to infer species
 relationships. For the maximum likelihood tree, we used IQtree 2. We
 determined the optimal substitution model for each locus (-m TESTONLY)
 first and then analyzed the partitioned, concatenated alignment with 1000
 ultrafast bootstrap replicates. We generated a species tree with
 SVDQuartets in Paup v4.0a166. We analyzed all quartet possibilities (n =
 16,356 quartets) and assessed node support with 100 bootstrap
 replicates.
description: # Data from: What is an eared nightjar? Ultraconserved elements clarify
 the evolutionary relationships of Eurostopodus and Lyncornis nightjars
 (Aves: Caprimulgidae) Dataset DOI:
 [10.5061/dryad.xksn02vrh](10.5061/dryad.xksn02vrh) ## Description of the
 data and file structure #### File: TableS1_sampling-table.zip
 **Description:** This is a zipped file containing Table S1, an
 Excel-formatted file of the samples used in this study and basic
 information about their quality (UCE loci and mean contig length).   ####
 File: Eurostopodus27_75percent_partitioned_iqtree.tre
 **Description:** Tree file from Figure 2, the IQtree inferred ML
 phylogeny. Note that the tip names were updated for correct taxonomy in
 Figure 2.  #### File: Eurostopodus27_75percent_partitioned_SVDQuartets.tre
 **Description:** Tree file from Figure 3, the SVDQuartets inferred
 phylogeny.   #### File: partitions_75per_IQtree-formatted.phylip
 **Description:** Partitions for the concatenated 75% complete UCE matrix
 that was the input file for the IQtree analysis.  #### File:
 Eurostopodus27_mafft_trim_75per_concat-IQtree-formatted.phylip
 **Description:** concatenated 75% complete UCE matrix that was the input
 file for the IQtree analysis.  #### File:
 Eurostopodus27_mafft_trim_75per_concat_SVDQuartets.nexus
 **Description:** Input file for the SVDQuartets analysis with proper
 taxon, charactersets, and taxonpartitioned sections. It will require
 appropriate flags on the command line in Paup, including to analyze all
 possible quartets and 100 BS replicates.  ## Code/software Excel (sampling
 table), a tree-viewing program (i.e., FigTree for files ending in .tre),
 and a text editing software (for .phylip and .nexus files).