ORCID Profile
0000-0002-7031-0747
Current Organisation
Victoria University of Wellington
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Publisher: Wiley
Date: 28-05-2019
DOI: 10.1111/EVA.12811
Publisher: Springer Science and Business Media LLC
Date: 03-12-2022
DOI: 10.1038/S41437-022-00579-1
Abstract: Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern ( n = 350) and ancient ( n = 26) mitochondrial genomes from Australasian snapper ( Chrysophrys auratus ) s led in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic ersity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide ersity and haplotype ersity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide ersity over the last 750 years ( p = 0.343), with no detectable loss of ersity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that erged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
Publisher: Informa UK Limited
Date: 13-07-2021
Publisher: Authorea, Inc.
Date: 03-10-2023
Publisher: Wiley
Date: 13-07-2020
DOI: 10.1002/ECE3.6558
Abstract: The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used or cause s les to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering s les unusable for applications such as genome‐wide sequencing. Nonetheless, little is known about the impact of suboptimal s ling conditions. We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25 M EDTA, NaCl saturated solution, and 2. Ethanol .5%) under a range of storage conditions over a three‐month period (s ling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus . We found that the storage solution has a strong effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hr, making s les unsuitable for next‐generation sequencing. Here, we conclude that DESS was the most promising solution when storing s les for genomic applications. We recognize that the best preservation protocol is highly dependent on the organism, tissue type, and study design. We highly recommend performing similar experiments before beginning a study. This study highlights the importance of testing s le preservation protocols and provides both practical and economical advice to improve DNA preservation when s ling for genome‐wide applications.
No related grants have been discovered for Tom Oosting.