DOI: 10.5061/dryad.3ffbg79xw
title: Population structure and genetic diversity analyses reveal isolation that may imperil the northernmost colony of the endangered Australian sea lion

description: Marine environments are experiencing rapid warming, substantially altering
 ecosystems. Populations at the edge of a species’ range are more
 vulnerable to environmental change as they are first affected and may have
 limited dispersal opportunities. This vulnerability may be exacerbated in
 species with specialised foraging and breeding strategies. The Australian
 sea lion (Neophoca cinerea) is an endangered otariid species that breeds
 across a ~3000 km range in southern Australia. At the most north-westerly
 edge of the species’ distribution, Australian sea lions breed across
 multiple islands within the Houtman Abrolhos Archipelago, Western
 Australia, a tropical-temperate location affected by marine heatwaves.
 This study aimed to examine the genetic structure and diversity of the
 Australian sea lions from the Houtman Abrolhos Archipelago compared to
 other populations in the species’ range. One hundred and twenty-five
 individuals, nineteen from Houtman Abrolhos, were genotyped from nineteen
 sample sites across Western Australia and South Australia. Our findings
 showed that individuals from the Houtman Abrolhos grouped into a single
 population, which was highly differentiated and had extremely low genetic
 diversity. The isolation and limited genetic variation of the Houtman
 Abrolhos Australian sea lion population suggest that it is extremely
 vulnerable to extirpation. Our study highlights the vulnerability of
 isolated populations of a species to rapid environmental change and
 stochastic events.
description: # Population structure and genetic diversity analyses reveal isolation
 that may imperil the northernmost colony of the endangered Australian sea
 lion Dataset DOI:
 [10.5061/dryad.3ffbg79xw](https://doi.org/10.5061/dryad.3ffbg79xw) ##
 Description of the data and file structure ### Files and variables ####
 File: ASL_Abrolhos_code **Description:** Text file containing R code used
 to complete analysis. #### File: pop_ID_metadata_ALL.csv
 **Description:** Metadata for each individual. Variables include, id
 (individual), sex, population (sample colony location), lat, long,
 metapopulation, state, age, date collected, plate details and dataset ID.
 #### File: Report_DNeof24-8961_1_moreOrders_SNP_mapping_2.csv
 **Description:** This is the SNP export file received from Diversity
 Arrays Technology. SNP 1 Row Mapping Format: "0" = Reference
 allele homozygote, "1" = SNP allele homozygote, "2"=
 heterozygote and "-" = double null/null allele homozygote
 (absence of fragment with SNP in genomic representation) DNeof22-7634:
 order 1 DNeof24-8961: order 2 | AlleleID | Unique identifier for the
 sequence in which the SNP marker occurs | | :-------------- |
 :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | AlleleSequence | In 1 row format: the sequence of the Reference allele. In 2 rows format: the sequence of the Reference allele is in the Ref row, the sequence of the SNP allele in the SNP row | | AvgCountRef | The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the Reference allele row | | AvgCountSnp | The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the SNP allele row | | AvgPIC | The average of the polymorphism information content (PIC) of the Reference and SNP allele rows | | CallRate | The proportion of samples for which the genotype call is either "1" or "0", rather than "-"  | | CloneID | Unique identifier for the sequence in which the SNP marker occurs | | FreqHets | The proportion of samples which score as heterozygous | | FreqHomRef | The proportion of samples which score as homozygous for the Reference allele | | FreqHomSnp | The proportion of samples which score as homozygous for the SNP allele | | OneRatioRef | The proportion of samples for which the genotype score is "1", in the Reference allele row | | OneRatioSnp | The proportion of samples for which the genotype score is "1", in the SNP allele row | | PICRef | The polymorphism information content (PIC) for the Reference allele row | | PICSnp | The polymorphism information content (PIC) for the SNP allele row | | RepAvg | The proportion of technical replicate assay pairs for which the marker score is consistent | | SNP | In 2 rows format: this column is blank in the Reference row, and contains the base position and base variant details in the SNP row. In 1 row format: contains the base position and base variant details | | SnpPosition | The position (zero indexed) in the sequence tag at which the defined SNP variant base occurs | | TrimmedSequence | Same as the full sequence, but with removed adapters in short marker tags |