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SRX13042177: UCE target enrichment of Pseudomyrmex_fervidus_D0861_GTTACGCA+AAGTGTCG (CASENT0220663) [Raw reads].
1 ILLUMINA (Illumina HiSeq 2500) run: 1.7M spots, 429.3M bases, 230Mb downloads

Design: DNA was extracted from single ants, either adults or pupae, using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA), and quantified with a Qubit fluorometer (HS Assay Kit, Life Technologies Inc., Carlsbad, CA). We sheared 5-50 ng input DNA to a target size of ~600 bp using either a Diagenode BioRuptor (Diagenode Inc., Denville, NJ) or QSonica Q800R3-110 (Qsonica Inc., Newtown, CT). Sheared DNA was input into a modified library prep procedure utilizing Kapa Hyper Prep kits (Roche Sequencing, Kapa Biosystems, Wilmington, MA) and custom dual-indexing adapters (Glenn et al. 2019). All library preparation steps were performed at quarter volume except for PCR, which was done at full volume. We cleaned libraries using 1.0x SPRI beads and quantified the cleaned products with Qubit. Enrichment of UCE loci was carried out using taxon-specific versions of the Hymenoptera v2 UCE probeset (Branstetter et al. 2017), which targets up to 2,590 UCE loci in Hymenoptera. Most taxa were enriched using the ant-specific version of the probe set, but three samples were enriched using a bee-ant-specific version (Grab et al. 2019). The probes and enrichment kit were purchased from Arbor Biosciences (Ann Arbor, MI). Enrichment was performed following either a standard UCE protocol (enrichment protocol v1.5 available at ultraconserved.org), based on Blumenstiel et al. (2010), or by using a modified protocol in which we followed Arbor Biosciences v3.02 protocol for enrichment day 1, and the standard UCE protocol for day 2. For the procedure we combined up to 10 samples into equimolar enrichment pools and used 500 ng of DNA for the hybridization reaction, which was carried out over 24 hours at 65C. Following enrichment, each pool was quantified via qPCR and then pooled into a final sequencing pool of 100 to 110 samples. Sequencing pools were sent to either the University of Utah Genomics Core for sequencing on an Illumina HiSeq 2500 or Novogene (Novogene Inc., Sacramento, CA) for sequencing on an Illumina HiSeq X.
Submitted by: USDA, Agricultural Research Service
Study: Species paraphyly and social parasitism: phylogenomics, morphology, and geography clarify the evolution of the Pseudomyrmex elongatulus group (Hymenoptera: Formicidae), a Mesoamerican ant clade
show Abstracthide Abstract
Using genetic, morphological, and geographical evidence, we investigate the species-level taxonomy and evolutionary history of the Pseudomyrmex elongatulus group, a clade of ants distributed from southwestern United States to Costa Rica. Through targeted enrichment of 2,524 UCE (ultraconserved element) loci we generate a phylogenomic data set and clarify the phylogenetic relationships and biogeographic history of these ants. The crown group is estimated to have originated about 8 Ma, in Mexico and/or northern Central America, and subsequently expanded into southern Central America and the southwestern Nearctic. The P. elongatulus group contains a mix of low- and high-elevation species, and there were apparently multiple transitions between these habitat types. We uncover three examples of one species-of restricted or marginal geographical distribution-being embedded phylogenetically in another species, rendering the latter paraphyletic. One of these cases involves an apparent workerless social parasite that occurs sympatrically with its parent species, with the latter serving as host. This suggests a sympatric origin of the parasite species within the distribution range of its host. Species boundaries are tested using three molecular delimitation approaches (SODA, bPTP, BPP) but these methods generate inflated species estimates (26-46 species), evidently because of a failure to distinguish population structure from species differences. In a formal taxonomic revision of the P. elongatulus group, based on almost 3,000 specimens from about 625 localities, we allow for geographic variation within species and we employ distinctness-in-sympatry criteria for testing hypotheses about species limits. Under these guidelines we recognize 13 species, of which nine are new: P. arcanus, sp. nov. (western Mexico); P. capillatus, sp. nov. (western Mexico); P. cognatus, sp. nov. (Chiapas, Mexico to Nicaragua); P. comitator, sp. nov. (Chiapas, Mexico); P. ereptor, sp. nov. (Veracruz, Mexico); P. exoratus, sp. nov. (southeastern Mexico, Honduras); P. fasciatus, sp. nov. (Chiapas, Mexico to Costa Rica); P. nimbus, sp. nov. (Costa Rica); and P. veracruzensis, sp. nov. (Veracruz, Mexico). Our study highlights the value of combining phylogenomic, phenotypic, and geographical data to resolve taxonomic and evolutionary questions.
Sample:
SAMN22841765 • SRS10979496 • All experiments • All runs
Library:
Name: Pseudomyrmex_fervidus_D0861
Instrument: Illumina HiSeq 2500
Strategy: WGS
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 1.7M spots, 429.3M bases, 230Mb
Run# of Spots# of BasesSizePublished
SRR168490901,717,105429.3M230Mb2022-11-01

ID:
17748432

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