What is an eared nightjar? Ultraconserved elements clarify the evolutionary relationships of Eurostopodus and Lyncornis nightjars (Aves: Caprimulgidae)

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 th..., 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 Eurostopodus species, including three species that have never been part of a molecular analysis before—two of which (E. exul and E. diabolicus) 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 in silico. 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 boo..., , # 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 ...,