UCE target enrichment of Andrena-nivalis-HC138: adult body/tissue. - SRA

SRX4041946: UCE target enrichment of Andrena-nivalis-HC138: adult body/tissue.
1 ILLUMINA (Illumina HiSeq 2500) run: 2.8M spots, 698M bases, 356.9Mb downloads

Design: DNA was extracted from pinned specimens of all 88 observed species. Extractions were performed using either a standard phenol-chloroform method, as detailed in Danforth (42) (most specimens), or using a Qiagen DNeasy Blood and Tissue Kit, with the proteinase-k incubation performed overnight (up to 12 hours). DNA concentration was measured using a Qubit 3.0 fluorometer (Thermo Fisher Scientific) and up to 50 ng of input DNA was sheared with a Qsonica Q800R2 sonicator to a mean fragment size of 400600 bp (60120 secs shear time, 25% amplitude, 1010 sec pulse). Illumina sequencing libraries were generated for each sample using Kapa Hyper Prep Kits and custom, dual-indexing adapters (43). Libraries were PCR amplified for 12 cycles, purified using an Ampure XP substitute (44), and quantified using Qubit. To enrich UCE loci, 1011 samples were pooled at equimolar concentrations and then up to 500 ng of each pool was enriched following the manufacturers protocol for day 1 (MYcroarray enrichment protocol v3.02) and the standard UCE protocol for day 2 (enrichment protocol v1.5 available at ultraconserved.org). For each enrichment, the custom bait set was diluted 1:4 (1 _L bait, 4 _L H2O) and the enrichment incubation was performed at 65C for 24 hrs. Following enrichment, each pool was PCR amplified for 18 cycles, purified using Ampure substitute, and quantified using Qubit and qPCR (Kapa Library Quantification Kit). Enriched pools were combined into a final sequencing pool and sent to the University of Utah genomics core facility for sequencing on an Illumina 2500 instrument (PE125, v4 chemistry).

Submitted by: USDA-ARS

Study: Agriculturally dominated landscapes reduce bee phylogenetic diversity and pollination services

PRJNA454902 • SRP144610 • All experiments • All runs

show Abstracthide Abstract

Agriculturally driven land use change threatens global biodiversity and has the potential to reshape the tree of life by favoring the persistence of some lineages over others. Yet it is unclear if loss of phylogenetic diversity compromises the delivery of ecosystem services. To address this critical knowledge gap, we combine extensive land cover, pollinator survey and crop data with a complete time-calibrated phylogenomic tree for this diverse bee community. Pollinator communities in highly agricultural landscapes contain 230 million fewer years of evolutionary history and loss of pollinator phylogenetic diversity was strongly associated with reduced crop yield and quality. Our study is the first to link landscape mediated changes in the phylogenetic structure of natural communities to the disruption of ecosystem services. Practices that measure their success only by the number of species conserved may fail to protect the full diversity of life impacted by these stressors.

Sample:

SAMN09061384 • SRS3259416 • All experiments • All runs

Organism: Andrena nivalis

Library:

Name: Andrena-nivalis-HC138

Instrument: Illumina HiSeq 2500

Strategy: WGS

Source: GENOMIC

Selection: Hybrid Selection

Layout: PAIRED

Runs: 1 run, 2.8M spots, 698M bases, 356.9Mb

Run	# of Spots	# of Bases	Size	Published
SRR7120383	2,791,919	698M	356.9Mb	2019-01-01

ID:: 5519042

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