U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX14207145: UCE target enrichment of Nomada_vincta_utahensis_BLX1520_ATGGTTGC+TCTGAGAG [Raw reads]
1 ILLUMINA (Illumina HiSeq X) run: 5.3M spots, 1.6G bases, 562.9Mb downloads

Design: DNA was extracted from pinned specimens using non-destructive methods and Zymo Quick-DNA Miniprep Plus Kits (Zymo Research, Irvine, CA, USA). We used a bee-ant specific probe set (Grab et al., 2019), which is just a subset version of the principal (Branstetter et al., 2017), to enrich 2,545 UCE loci. The probes are synthesized and available through Arbor Biosciences (Ann Arbor, MI, USA). Extracted samples were first sheared to fragment sizes of ~400-600 bp using a Qsonica sonicator (Q800R2; Qsonica, Newton, CT, USA). Older samples were not sheared due to their already degraded status; all other samples were sonicated for either 30, 60, or 90 seconds depending on their quality. Illumina libraries were generated using KAPA HyperPrep kits (Roche Sequencing, Pleasanton, CA, USA) and custom dual-indexing adapters (Glenn et al., 2019). Fragmented DNA was purified and concentrated using an in house paramagnetic-bead solution (Rohland & Reich, 2012). Once the final bead cleaning was complete, sample DNA concentration was measured using a Qubit 3 fluorometer and then pooled into 12 groups containing 9-10 samples of equimolar concentrations. Enrichment of the samples followed protocols from both Arbor Biosciences (v4 protocol; day1) and a standard UCE protocol (Blumenstiel et al., 2010; day 2) split over two consecutive days. After enrichment, each pool was quantified using qPCR, combined into one sample and then sent off for sequencing. For trimming raw reads, use i7:GATCGGAAGAGCACACGTCTGAACTCCAGTCAC*ATCTCGTATGCCGTCTTCTGCTTG and i5:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT*GTGTAGATCTCGGTGGTCGCCGTATCATT where * indicates the index sequence.
Submitted by: York University
Study: Molecular phylogeny and historical biogeography of the cleptoparasitic bee genus Nomada (Hymenoptera: Apidae) using ultraconserved elements
show Abstracthide Abstract
The genus Nomada Scopoli (Hymenoptera: Apidae) is the largest genus of brood parasitic bees with nearly 800 species found across the globe and in nearly all biogeographic realms except Oceania and Antarctica. There is no previous molecular phylogeny focused on Nomada despite their high species abundance nor is there an official biogeography. Using ultraconserved element (UCE) phylogenomic data, we constructed the first molecular phylogeny for the genus Nomada and tested the previously established 16 species groups. We also estimated divergence dates using fossil calibration points and inferred the origin and diversification of this genus around the globe. Our phylogeny provided support for 14 of the 16 previously established species groups; two species groups were suggested to be one unified group while another group was found to be paraphyletic. All remaining species groups were found to be monophyletic. Historical biogeographic reconstruction indicates that Nomada originated in the Holarctic, but most likely in the Palearctic ~65 Mya. Geodispersal into the southern hemisphere occurred three times; once during the Eocene into the Afrotropics, once during the Oligocene into the Neotropics, and once during the Miocene into Australasia. Geodispersal across the Holarctic was most frequent and occurred repeatedly throughout the Cenozoic era, using the De Geer, Thulean, and the Bering Land Bridges. This is the first instance of a bee using both the Thulean and De Geer land bridges and has implications of how early bee species dispersed throughout the Palearctic in the late Cretaceous and early Paleogene.
Sample:
SAMN21502208 • SRS12029207 • All experiments • All runs
Library:
Name: Nomada_vincta_utahensis_BLX1520_ATGGTTGC+TCTGAGAG
Instrument: Illumina HiSeq X
Strategy: WGS
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 5.3M spots, 1.6G bases, 562.9Mb
Run# of Spots# of BasesSizePublished
SRR180551235,337,0621.6G562.9Mb2022-03-30

ID:
20072392

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...