| Summary: | 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) ...
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