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SRX10167168: UCE target enrichment of Parepeolus_aterrimus_EX024_GTCCTTCT+AGACGCTA [Raw reads]
1 ILLUMINA (HiSeq X Ten) run: 2.3M spots, 683.7M bases, 239.5Mb downloads

Design: We used a targeted UCE approach to generate sequence data following previous literature (Faircloth et al. 2012, 2015). The protocols used followed those outlined in Branstetter et al. (2017) and were carried out at the USDA-ARS bee research lab in Logan, Utah, USA. We targeted a set of 2,527 UCE loci and additional legacy loci using baits based on the Hymenoptera v2 probe set outlined by Branstetter et al. (2017), with ant-bee specific probes as described in Grab et al. (2019). Probes were synthesized by Arbor Biosciences, previously MYcroarray. First, extracted DNA samples were sheared to reduce the average fragment size to a target of ~400-600 bp. Older or more degraded samples were not sheared, while other samples were sheared in a Q800R3 sonicator (Qsonica) for 30, 60, or 90 seconds depending on sample quality and predicted size distribution. Mean final DNA input mass for all samples was 102 ng but ranged from <1 ng 1,630 ng. Library preparation involved the use of a KAPA HyperPrep kit (Roche Sequencing Systems) for enzymatic steps including repair of fragment ends and addition of A-tails, and Illumina TruSeq-style adapters (Glenn et al. 2019) for dual-indexing with redundantly unique sequences. DNA-binding magnetic beads were made following an in-house protocol based on Rohland and Reich (2012) and were used to clean and concentrate samples at various steps in the process. After the final bead cleaning, samples were measured for DNA concentration with a Qubit 3 fluorometer and pooled in groups of 8-10 at equimolar concentrations. These pooled samples were enriched following a protocol from Arbor Biosciences (v4) for the first day of UCE enrichment, and a standard UCE protocol for the second day (enrichment protocol v1.5 available at ultraconserved.org, based on Blumenstiel et al. (2010)). Post-enrichment samples were measured on a TapeStation machine for fragment size distributions and size selected with a Blue Pippin machine (Sage Science) for a range of 200-700 base pairs, if necessary. Finally, pooled libraries were quantified with an Applied Biosystems qPCR machine and KAPA reagents, pooled together, and sent off for sequencing.
Submitted by: Cornell University
Study: Phylogenetic relationships and the evolution of host preferences in the largest clade of brood parasitic bees (Apidae: Nomadinae)
show Abstracthide Abstract
Brood parasites (also known as cleptoparasites) represent a substantial fraction of global bee diversity. Rather than constructing their own nests, these species instead invade those of host bees to lay their eggs. Larvae then hatch and consume the food provisions intended for the host's offspring. While this life history strategy has evolved numerous times across the phylogeny of bees, the oldest and most speciose parasitic clade is the subfamily Nomadinae (Apidae). However, the phylogenetic relationships among brood parasitic apids both within and outside the the Nomadinae have not been fully resolved. Here, we present new findings on the phylogeny of this diverse group of brood parasites based on ultraconserved element (UCE) sequence data and extensive taxon sampling. We suggest a broader definition of the subfamily Nomadinae to describe a clade that includes almost all parasitic members of the family Apidae. The tribe Melectini forms the sister group to all other Nomadinae, while the remainder of the subfamily is composed of two sister clades: a "nomadine line" representing the former Nomadinae sensu stricto, and an "ericrocidine line" that unites several, mostly Neotropical, lineages. We find the tribe Osirini Handlirsch to be polyphyletic, and divide it into three lineages, including the newly described Parepeolini trib. nov. In addition to our taxonomic findings, we use our phylogeny to explore the evolution of different modes of parasitism, detecting two independent transitions from closed-cell to open-cell parasitism. Finally, we examine how nomadine host-parasite associations have evolved over time. In support of Emery's rule, which suggests close relationships between hosts and parasites, we confirm that the earliest nomadines were parasites of their close free-living relatives within the family Apidae, but that over time their host range broadened to include more distantly related hosts spanning the diversity of bees.
Sample:
SAMN17506911 • SRS8317659 • All experiments • All runs
Library:
Name: Parepeolus_aterrimus_EX024_GTCCTTCT+TAGCGTCT
Instrument: HiSeq X Ten
Strategy: WGS
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 2.3M spots, 683.7M bases, 239.5Mb
Run# of Spots# of BasesSizePublished
SRR137816282,278,897683.7M239.5Mb2021-05-24

ID:
13294744

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