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SRX1458153: UCE target enrichment of Abroscopus-albogularis-KU-28164: muscle/liver tissue
1 ILLUMINA (Illumina HiSeq 2500) run: 1.1M spots, 212.7M bases, 89.6Mb downloads

Design: We sheared 500 ng of DNA of each sample (except for one sample extracted from the toepad of a museum study skin, which was not sheared) to 400Đ600 bp in 50 _l volume using a Covaris S220 sonicator at 175 W peak incident power, 2% duty factor, and 200 cycles per burst for 45 seconds. We performed end repair, A-tailing, adapter ligation, and amplification on sheared DNA using Kapa Biosystems Library Prep kits following the procedure of Faircloth et al. (2012) described in detail at http://ultraconserved.org. We deviated from the standard protocol by using _ volume of reagents called for in the library prep kit, ligating universal iTru stubs instead of sample-specific adapters to allow for dual indexing, and adding a second AMPure XP bead clean up at 1.0x volume after stub ligation. We incorporated dual-indexes to library fragments using a 17-cycle PCR with NEB Phusion High-Fidelity PCR Master Mix. iTru stubs and adapters were developed and designed by T. Glenn et al (unpublished data). We quantified libraries using a Qubit 2.0 Fluorometer and pooled sets of eight samples at equimolar ratios for enrichment. We performed sequence capture and post-enrichment amplification following standard protocols (Faircloth et al. 2012) using the Mycroarray MYbaits kit for Tetrapods UCE 5K version 1, which targets 5,060 UCE loci. We hybridized biotinylated RNA probes with pooled libraries for 24 hrs., and which we enriched DNA targets using streptavidin-coated beads. We amplified fragments with a 17-cycle PCR amplification step using NEB Phusion High-Fidelity PCR Master Mix. After post-enrichment amplification, we quantified libraries using an Illumina Eco qPCR System and a commercial library quantification kit (Kapa Biosystems, Inc.), combined 96 libraries into a 10 ľM pool, and sequenced the pooled libraries in a high output, paired-end run of 100 cycles on an Illumina HiSeq 2500 System at the University of Kansas Genome Sequencing Core.
Submitted by: Louisiana State University
Study: Tectonic collision and uplift of Wallacea triggered the global songbird radiation
show Abstracthide Abstract
Songbirds (oscine passerines) are the most species rich and cosmopolitan bird group, comprising almost half of global avian species diversity. Because of their diversity and ubiquity, songbirds are used extensively in studies of evolutionary ecology, diversification, and ethology. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Prior research suggested songbird diversification scenarios that are largely uncoupled from Earth history, including extensive diversification of lineages in New Guinea prior to its emergence as a landmass and long-distance dispersal to Africa or Asia when no dispersal corridors existed. However, these results may be flawed because the studies relied on unresolved phylogenetic relationships and a controversial biogeographic time calibration. Here, we combine the first genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide the first well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred after island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Although New Guinea presently contains high songbird species richness, our data unambiguously falsify the proto-Papuan hypothesis for early songbird diversification2,6 and suggest that New Guinea has, instead, served as an “evolutionary refuge” for Australian lineages that have diversified more recently within the island23. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent.
Sample:
SAMN04301695 • SRS1185696 • All experiments • All runs
Library:
Name: Abroscopus-albogularis-KU-28164
Instrument: Illumina HiSeq 2500
Strategy: WGS
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 1.1M spots, 212.7M bases, 89.6Mb
Run# of Spots# of BasesSizePublished
SRR29687651,053,098212.7M89.6Mb2016-12-01

ID:
2060606

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