Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus)

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) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity 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 diverged 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.

Five millennia of mitochondrial introgression in Atlantic bluefin tuna identified using ancient DNA

“…Ancient and modern samples largely intermixed in all analyses, suggesting mitogenomic stability and temporal continuity through time. Similar observations in other species, such as Atlantic cod (Gadus morhua) (Martínez- García et al, 2021) and New Zealand snapper (Chrysophrys auratus) (Oosting et al, 2023) emphasize the low power of the MT genome to observe spatiotemporal differentiation in wide ranging fish species. The regular presence of identical haplotypes across sampling locations and temporal cohorts emphasizes the lack of mitogenomic variation and informative markers for population structure in this species.…”

“…For example, the presence of introgressed MT haplotypes may dominate genealogies with recent dispersal history and thereby overshadow genetic signals from past dispersal events (Sloan et al, 2017; Ballard & Whitlock, 2004). Presence of introgressed, heterospecific alleles and haplotypes will also affect population genomic analyses by inflating measures of genetic diversity and divergence (Oosting et al, 2023; Rodriguez & Krug, 2022; Wang et al, 2022; Hawks, 2017). Avoiding such inflation is important because these statistics can influence management choices (Willi et al, 2022; Hohenlohe et al, 2021; Kardos et al, 2021) and inflated measures of genetic diversity or effective population size may exaggerate the genetic robustness of a truly vulnerable population.…”

“…), high rates of introgressive hybridization (15% of all samples) have been found between two species ( S. fasciatus and S. mentella ) that live sympatrically in hybrid zones and yet maintain their morphology, resembling one of the parent species (Benestan et al, 2021; Roques et al, 2001). Likewise, introgression has been observed in European seabass ( Dicentrarchus labrax ) (Duranton et al, 2020; Vandeputte et al, 2019), capelin ( Mallotus villosus ) (Cayuela et al, 2020; Colbeck et al, 2011), European anchovy ( Engraulis encrasicolus ) (Le Moan et al, 2016), Australasian snapper ( Chrysophrys auratus ) (Oosting et al, 2023) and Atlantic and Pacific herring ( Clupea harengus and C. pallasii ) (Semenova, 2020).…”