DOI: 10.5061/dryad.xwdbrv1q9
title: Postglacial recolonization of the Southern Ocean by elephant seals occurred from multiple glacial refugia

description: The Southern Ocean is warming more rapidly than other parts of our planet.
 How this region’s endemic biodiversity will respond to such changes can be
 illuminated by studying past events, through genetic analyses of
 time-series data sets including historic and fossil remains.
 Archaeological and subfossil remains show that the southern elephant seal
 (Mirounga leonina) was common along the coasts of Australia and New
 Zealand in the recent past. This species is now mostly confined to
 sub-Antarctic islands and the southern tip of South America. We analysed
 ancient seal samples from Australia (Tasmania), New Zealand, and the
 Antarctic mainland to examine how southern elephant seals have responded
 to a changing climate and anthropogenic pressures during the Holocene. Our
 analyses show that these seals formed part of a broader Australasian
 lineage, comprising seals from all sampled locations from the south
 Pacific sector of the Southern Ocean. Our study demonstrates that southern
 elephant seal populations have dynamically altered both range and
 population sizes under climatic and human pressures, over surprisingly
 short evolutionary timeframes for such a large, long-lived mammal.
description: <em>Control Region Sequence Analysis:</em> Partial
 control region (HVR1) sequences were successfully amplified from modern
 and ancient samples. A data set with representative sequences from various
 populations was constructed. Genetic diversity metrics were calculated,
 and F<sub>ST</sub> values were used to measure genetic
 differentiation. AMOVAs were performed to infer geographic structure. A
 time-sensitive haplotype network was constructed.
 <em>Mitochondrial Genome Assembly:</em> DNA
 extraction was performed on selected ancient samples for mitochondrial
 genome assembly. Libraries were prepared, quantified, and enriched using
 hybridization capture with bait from a closely related species. PCR
 amplification and pooling of samples were performed and sequenced using
 the Illumina MiSeq platform. <em>Data
 Processing:</em> Sequence data were processed using specific scripts
 to trim adapters, merge overlapping read pairs, and filter low-quality
 reads. The processed reads were mapped to a reference mitochondrial genome
 using BWA and filtered for quality and duplicates. Consensus sequences
 were computed, and patterns of post-mortem DNA damage were assessed using
 MapDamage (SI Appendix). <em>Phylogenetic
 Analysis of Mitogenome Sequences: </em>Newly generated mitogenome
 sequences were aligned with global southern elephant seal
 sequences.  We also used Bayesian analysis in BEAST
 v1.8.2 (Suchard et al. 2018) to compare three models of post-mortem
 sequence damage: no damage, age-dependent damage, and age-independent
 damage (Ho et al., 2007; Rambaut et al., 2009; Ho, 2012). Models were
 compared using marginal likelihoods estimated by stepping-stone sampling
 (Xie et al., 2010). Posterior distributions of parameters were estimated
 using Markov Chain Monte Carlo sampling over 75 million steps, with
 samples drawn every 10<sup>4</sup> steps.
  To infer a dated phylogenetic tree, we performed a Bayesian
 molecular dating analysis in BEAST. We used a Skyride coalescent tree
 prior (for species with a dynamic population history) and a strict
 molecular clock, selected by comparison of marginal likelihoods calculated
 by stepping-stone sampling. Estimates of node times were calibrated using
 the sample dates for the ancient Tasmanian, New Zealand, and Victoria Land
 Coast sequences. We also fixed the mutation rate of HVR1 based on an
 estimate from a previous study of the southern elephant seal (de Bruyn et
 al., 2009). Posterior distributions of parameters were estimated using
 Markov Chain Monte Carlo sampling over 75 million steps, with samples
 drawn every 10<sup>4</sup> steps. We ran the analysis in
 duplicate to check for convergence and combined the samples after
 discarding the first 10% as burn-in. Sufficient sampling was confirmed by
 inspecting the samples in Tracer v1.7.1 (Rambaut et al., 2018).
 See uploaded supplementary information to Zenodo entry for full
 methodologies.
description: # Postglacial recolonization of the Southern Ocean by elephant seals
 occurred from multiple glacial refugia
 [https://doi.org/10.5061/dryad.xwdbrv1q9](https://doi.org/10.5061/dryad.xwdbrv1q9) ## Description of the data and file structure ### Files and variables #### File: SES.ControlRegion.fasta **Description:** Alignment of 628 previously published and newly generated ancient and modern mitochondrial control region sequences of southern elephant seals (*Mirounga leonina*) from all known living and extinct populations around the Southern Ocean. Each sequence name has a dollar sign followed by an age category (this info is for the temporal haplotype network and can be deleted). #### File: SES.Mitogenomes.fasta **Description:** Alignment of 23 previously published and newly generated ancient and modern mitogenomes of southern elephant seals (*Mirounga leonina*) from living and extinct populations from Victoria Land Coast (Antarctica), Macquarie Island, Tasmania and New Zealand. This was the data set used for the BEAST analysis.  Supporting information: * Berg_et_al_Supp_Info_final_revised_130225.docx: contains detailed methodologies ## Code/software Any freely available DNA sequence alignment or text edit software. ## Access information Other publicly accessible locations of the data: * GenBank - newly generated mitogenomes are PQ776891- PQ776911, and newly generated mitochondrial control region sequences are PQ773320- PQ773356. Data was derived from the following sources: * Some sequences were downloaded from GenBank originating from the following studies: * Arnason, U., Gullberg, A., Janke, A., Kullberg, M., Lehman, N., Petrov, E.A. Vainola, R. (2006) Pinniped phylogeny and a new hypothesis for their origin and dispersal.  *Molecular Phylogenetics and Evolution,* 41, 345-354. * Bogdanowicz, W., Pilot, M., Gajewska, M., Suchecka, E., Golachowski, M. (2013) Genetic diversity in a moulting colony of southern elephant seals in comparison with breeding colonies. *Marine Ecology Progress Series*, 478, 287–300. * Chauke, L.F. (2008) Genetic variation and population structure of southern elephant seals *Mirorunga leonina* from Marion Island. Unpublished MSc thesis, University of Pretoria. * Corrigan, L.J., Fabiani, A., Chauke, L., McMahon, C.R., de Bruyn, M., Bester, M.N., Bastos, A., Campagna, C., Muelbert, M.M., Hoelzel, A.R. (2016) Population differentiation in the context of Holocene climate change for a migratory marine species, the southern elephant seal. *Journal of Evolutionary Biology,* 29, 1667–1679. * de Bruyn, M., Hall, B.L., Chauke, L.F., Baroni, C., Koch, P.L., Hoelzel, A.R. (2009). Rapid response of a marine mammal species to Holocene climate and habitat change. *PLOS Genetics, 5, e1000554*. * Fabiani, A., Hoelzel, A. R., Galimberti, F., Muelbert, M.M.C. (2003) Long-range paternal gene flow in the southern elephant seal. *Science,* 299, 676–676. * Hoelzel, A., Halley, J., O'Brien, S.J., Campagna, C., Arnborm, T., Le Boeuf, B., Ralls, K., Dover, G. (1993) Elephant seal genetic variation and the use of simulation models to investigate historical population bottlenecks. *Journal of Heredity,* 84, 443–449. * Slade, R. W., Moritz, C., Hoelzel, A.R., Burton, H.R. (1998) Molecular population genetics of the southern elephant seal *Mirounga leonina*. *Genetics,* 149, 1945–1957.