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SRX15484970: UCE target enrichment of odontophorus_guttatus_FLMNH_4312
1 ILLUMINA (Illumina HiSeq 3000) run: 2.4M spots, 713.6M bases, 290.2Mb downloads

Design: We used 250 ng of sheared DNA in 25 uL volume to prepare dual-indexed genomic libraries of each sample at _ volume reactions using the KAPA Hyper Prep library preparation kit and custom indexes (Glenn et al., 2019). __We combined the libraries into pools containing between six and eight samples for enrichment, and we kept tissues and toepads in separate pools. We enriched each library pool for 5,060 UCE loci using a MYbaits_Tetrapods-UCE-5K kit. After enrichment, we performed 16 cycles of PCR recovery, removed adapter-dimers using a Qiagen GeneRead Size Selection Kit, and collected paired-end 150 bp sequence data from an Illumina HiSeq 3000.
Submitted by: Louisiana State University
Study: Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
show Abstracthide Abstract
As phylogenomics focuses on comprehensive taxon sampling at the species and subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, the Northern Bobwhite (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.
Sample: Odontophorus guttatus FLMNH 4312
SAMN22937515 • SRS13200621 • All experiments • All runs
Name: odontophorus_guttatus_FLMNH_4312
Instrument: Illumina HiSeq 3000
Strategy: WGS
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 2.4M spots, 713.6M bases, 290.2Mb
Run# of Spots# of BasesSizePublished


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