Published February 1, 2024 | Version v1
Dataset Restricted

Drennan 2024 Doctoral Thesis Chapter 5 dataset - SNP catalogs

Creators

  • 1. ROR icon University of Southampton
  • 2. Natural History Museum London
  • 3. ROR icon Universidad Complutense de Madrid
  • 4. ROR icon NORCE Norwegian Research Centre
  • 5. ROR icon University of Gothenburg

Description

This dataset supports the thesis entitled “Patterns of Diversity, Connectivity, and Evolution in Southern Ocean and Deep-Sea Annelids” by Regan Drennan
AWARDED BY: University of Southampton
DATE OF AWARD: 2024
 
DESCRIPTION OF THE DATA:
 
Genomic data generated in thesis Chapter 5: Population genomics, cryptic diversity and phylogeographic structure in the Southern Ocean circumpolar annelid, Aglaophamus trissophyllus (Annelida: Nephtyidae)
 
Single nucleotide polymorphism (SNP) genomic data was prepared and sequenced using a ddRADseq library preparation protocol (see Chapter 5 Results section 5.2.5 for more details). 
 
Following sequencing, filtering and locus assembly was carried out using Stacks v 2.64 https://catchenlab.life.illinois.edu/stacks/ - Stacks generates a catalog to determine which haplotype alleles are present at every locus in each individual. This dataset includes all catalogs analysed in thesis Chapter 5 following initial QC, processing, and quality filtering steps (see Chapter 5 Results section 5.2.5 for more details).
 
This dataset contains:
 
Four zipped catalog folders containing the final output of the Stacks “denovo_map.pl” de novo assembly pipeline. Each folder contains two major files, “catalog.fa.gz”, which contains the consensus sequence for each assembled locus in the data, as well as “catalog.calls”, a custom file that contains genotyping data. 
 
These files are intended to be read by the Stacks “populations” program, which can apply appropriate filters, calculate population genetic statistics, and export the data for further analyses, as in Chapter 5. 
 
The four catalog folders are as follows: 
 
All_species_600k_n113_catalog - combined catalog of all individuals across all putative species with >600k reads (113 individuals)
 
Agla1_Agla2_600k_n93_catalog - combined catalog for both putative species “Agla 1” and “Agla 2” individuals with >600k reads (93 individuals)
 
Agla1_600k_n73_catalog - catalog of putative species “Agla 1” individuals with >600k reads (73 individuals)
 
Agla3_600k_n28_catalog - catalog of putative species “Agla 2” individuals with >600k reads (28 individuals)
 
Date of data collection: Jan-Feb 2023
 
Information about geographic location of data collection: Southern Ocean, Antarctica (see Chapter 5 for location details)
 
Licence:
CC BY
 
Related projects/Funders:
NERC INSPIRE DTP
 
Related publication:
Drennan et al. 2024 in prep
 
Date that the file was created: Jan, 2024
 
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