Understanding patterns of evolution and divergence in populations is important for defining conservation units and informing taxonomy. However, when populations have low genetic diversity, or are closely related, genetic differentiation can be difficult to detect, particularly when relying on small numbers of genetic markers. Whole-genome sequencing allows for genome-wide identification of both neutral and outlier variation, improving the resolution of subtle population structure and providing insight into evolutionary processes. Here, we investigated genomic differentiation in a recently diverged and highly threatened albatross complex, the Antipodean ( D. antipodensis antipodensis ) and Gibson′s albatross ( D. a. gibsoni ), using genome-wide neutral and outlier datasets. Whole-genome resequencing of 86 individuals sampled across Antipodes Island ( D. a. antipodensis ) and the Auckland Islands ( D. a. gibsoni ) identified 381,176 neutrally evolving and 57 independently segregating outlier (putatively adaptive) SNPs. Analyses of both datasets revealed significant genetic differentiation between the Antipodean and Gibson′s albatross, no evidence of contemporary gene flow and evidence of selective sweeps suggesting local adaptation. Within-population structure was also identified for the Gibson′s albatross, with genetic differentiation among sample sites from different islands (Adams Island and Disappointment Island). Patterns of heterogenous differentiation across the genome suggest the taxa are on different evolutionary trajectories. Together with existing morphological and behavioural evidence, these genomic results support reassessment of their conservation and taxonomic status. More broadly, this study demonstrates the value of combining neutral and putatively adaptive genomic variation to resolve subtle population structure in recently diverged taxa.

Fisheries bycatch mortality is a significant threat facing seabirds worldwide. Yet, understanding which species are most impacted is hindered by uncertainties when identifying bycatch specimens. Birds can be damaged by fishing gear and closely related seabird taxa can have overlapping traits, presenting challenges for identification based on morphology and plumage. Here, we have developed a genetic method for identifying seabirds at risk from bycatch in Aotearoa New Zealand across 36 species including albatrosses, storm petrels, petrels, shags, and penguins. Cytochrome Oxidase I (COI) analysis enabled identification of all taxa to the genus level, and 75% to the species level. All but one species (Salvin's albatross, Thalassarche salvini) that could not be successfully identified using COI could be distinguished from their more highly variable mitochondrial control region sequences. Subspecies of Cape petrel (Daption capense capense/D. c. australe), Antipodean albatross (Diomedea antipodensis antipodensis/D. a. gibsoni), and Buller's albatross (T. bulleri bulleri/T. b. platei) could not be distinguished using either of these loci so will require development of more highly discriminating markers. Our methodology will be a valuable complement to the current formal identification process of seabird bycatch in South Pacific fisheries, helping to inform future fisheries management and seabird conservation.

Albatrosses are a highly threatened family of seabirds that are facing widespread declines, largely attributed to incidental fisheries bycatch mortality. Protection relies upon sound knowledge of distinct breeding units, but population structure has been difficult to detect due to low levels of genetic differentiation between closely related taxa. Whole-genome data have not yet been used to investigate this issue, and genomic resources for albatrosses are currently limited to a few fragmented genome assemblies. Here, we present high-quality reference genomes for both the Antipodean and Gibson's albatrosses (Diomedea antipodensis antipodensis and D. a. gibsoni), sequenced using Oxford Nanopore Technology and assembled with the Flye assembly algorithm. Both assemblies were around 1.25 Gb in length and comprised 255 and 313 scaffolds for the Antipodean and Gibson's assemblies, respectively. Although not chromosome-resolution assemblies the largest 60 scaffolds of each genome showed Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of ~ 97%. As well, most chromosomes are likely represented by only a few large scaffolds, as suggested by alignment of the two genomes, and alignment of each genome to an available chromosome-level assembly of Cory's shearwater (Calonectris borealis). These two high-quality reference genomes for albatross will allow population-level analysis of genomic diversity, gene flow, and adaptive diversity to inform taxonomy and conservation management in a changing world.

Phylosymbiosis describes an association between the phylogenetic relationships among host species and the composition of their microbiomes. Conifers have long evolutionary histories and extensive opportunity for coevolution to have occurred among these host plants and their microbiomes. We tested for phylosymbiosis in the root microbiomes of conifer seedlings as an indicator of coevolutionary plant-microbiome selection processes or concurrent ecological filtering. We grew 23 species of Pinaceae and Cupressaceae in a common soil for 52 weeks and assessed whether similarity in bacterial and fungal root microbiome composition was based on host phylogenetic distances using correlation and topology-based methods. Relationships among soil physicochemical properties, host traits, and microbial community composition were also assessed. Phylosymbiosis was significant in both bacterial and fungal root microbiomes. Host taxonomic relationships consistently explained more variance in microbiome composition than host traits or soil physicochemical properties. Indirect host effects on soil physicochemical properties, specifically sulfate sulfur, explained variation in microbiome composition in most models. We have evidence for phylosymbiosis in the root systems of conifer seedlings in both bacterial and fungal communities. This represents an important step toward uncovering patterns of coevolution in long-lived organisms and their associated microbes and indicates the fundamental role of phylosymbiosis in root microbiome assembly.Copyright (c) 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Aotearoa New Zealand’s swamp forests have experienced significant habitat loss in fewer than two hundred years. Many of the country’s tree species are endemic with sparse to no genetic information available to underpin conservation strategies. Syzygium maire, Aotearoa’s only endemic Syzygium species, is a culturally and ecologically important component of swamp forest habitats. Unfortunately, populations of S. maire have been greatly reduced, heavily fragmented and are susceptible to the emergent pathogen Austropuccinia psidii (myrtle rust), posing eminent danger of a further decline of the species. We sought to develop genomic resources to inform conservation management of S. maire. To this end, we used long read, high accuracy sequencing technology to produce a highly complete reference quality genome for S. maire. The genome sequence was named ‘Ngā Hua o te Ia Whenua’ by the local Māori tribe where the tree used for genome sequencing grows. We assess whether genome-level divergence with other Myrtaceae may have followed geographic isolation of the species. We detect conservation of large scale synteny between three Syzygium species and Eucalyptus grandis, providing support for the stability of Syzygium genomes across evolutionary time. We annotate genes implicated in fungal pathogen defence, identifying several hundred putative NLR genes, including putative homologs of previously identified Austropuccinia psidii resistance genes. Finally, we evaluate the genetic relationships of individuals of a small, isolated population of trees. We find evidence of high levels of kinship and inbreeding within small and isolated S. maire populations, informing local-scale conservation strategies for the species. Our findings enable practical conservation actions and provide resources for larger scale studies of S. maire and other Syzygium species in the future.

The identification of genetically distinct populations is central to the management and conservation of wild populations. Whole-genome-sequencing allows for high-resolution assessment of genetic structure, demographic connectivity and the impacts of selection acting on different parts of the genome. Here, we utilise population genomics to investigate the genetic structure of the Australasian snapper or Tāmure ( Chrysophrys auratus ), an ecologically, economically, and culturally important (taonga) marine fish. We analysed over four million high-quality SNPs obtained by whole-genome sequencing from 382 individuals collected across its New Zealand range. We identified two genetic clusters (an eastern and western cluster) with genetic disjunctions around on either side of the North Island of New Zealand. These genetic clusters do not match the current fisheries management areas. Pairwise-F and ADMIXTURE analyses showed the presence of directional gene flow occurring at both genetic disjunctions from the East to the West cluster. We hypothesize that major ocean currents are limiting the dispersal of snapper at these genetic disjunctions. The heterogeneous coastal environment is also likely driving evolutionary change. A genome scan identified four significantly divergent genomic regions between genetic clusters. A diverse pattern of genetic variation in these regions implies that different evolutionary processes drive local adaptation in these clusters. Identification of candidate genes in these regions also provides a tentative connection to which traits may be under selection. Our results provide novel insights into New Zealand’s coastal environment influences evolutionary processes, and valuable information for effective management of the snapper fisheries.

Investigations into niche dynamics and interspecific interactions are crucial to assess the vulnerability of threatened species to competition and environmental change. The Whenua Hou Diving Petrel Pelecanoides whenuahouensis is a critically endangered seabird, specializing in breeding in sand dunes in Aotearoa (New Zealand). The species is at risk from competition for burrow sites with the abundant, habitat‐generalist Common Diving Petrel Pelecanoides urinatrix chathamensis, among other terrestrial and near‐shore threats (storm‐induced erosion and vessel‐based light pollution). However, Whenua Hou Diving Petrel foraging niches at sea and associated threats are poorly understood. We sampled blood and feathers from both species on Whenua Hou (Codfish Island) during 2017–19 and used stable isotope (δ15N and δ13C) analyses to quantify foraging niche dynamics and interspecific interactions. During incubation periods, when birds are restricted by central place foraging, diving petrels exhibited clear niche segregation. Whenua Hou Diving Petrels were more generalist feeders with wider isotopic niches than Common Diving Petrels, which exhibited restricted isotopic niches and fed in neritic waters. During non‐breeding periods, foraging niches expanded, and segregation was reduced, as both species dispersed into the Southern Ocean. These patterns were largely consistent among years, despite varying climatic conditions. However, Common Diving Petrel foraging niches appeared to shrink during El Niño conditions, suggesting environmental sensitivity. In contrast, the consistently stable, generalist foraging niches of Whenua Hou Diving Petrels suggested potential limited sensitivity to competition and impacts of environmental change at sea. Recovery efforts should, therefore, focus on addressing the previously identified terrestrial and near‐shore threats.

Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management attains its sustainability goals. Here we generated 55 Gb of short Illumina reads (92× coverage) and 73 Gb of long Nanopore reads (122×) to produce the first genome assembly of the marine teleost tarakihi ( Nemadactylus macropterus ), a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq RNA reads were obtained from four tissue types of another specimen to assist in gene annotation. The final genome assembly was 568 Mb long and consisted of 1,214 scaffolds with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii BUSCOs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared to the same values reported for other fishes. Repetitive elements covered 30.45% of the genome and 20,169 protein-coding genes were annotated. Iso-Seq analysis recovered 91,313 unique transcripts (isoforms) from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly along with the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics, as well as comparative eco-evolutionary studies in other teleost and related organisms.

Tarakihi (Nemadactylus macropterus) is an important fishery species with widespread distribution around New Zealand and off the southern coasts of Australia. However, little is known about whether the populations are locally adapted or genetically structured. To address this, we conducted whole-genome resequencing of 175 tarakihi from around New Zealand and Tasmania (Australia) to obtain a dataset of 7.5 million genome-wide and high-quality single nucleotide polymorphisms (SNPs). Variant filtering, FST-outlier analysis, and redundancy analysis (RDA) were used to evaluate population structure, adaptive structure, and locus-environment associations. A weak but significant level of neutral genetic differentiation was found between tarakihi from New Zealand and Tasmania (FST = 0.0054–0.0073, P ≤ 0.05), supporting the existence of at least two separate reproductive stocks. No clustering was detected among the New Zealand populations (ΦST < 0.001, P = 0.77). Outlier-based, presumably adaptive variation suggests fine-scale adaptive structure between locations around central New Zealand off the east (Wairarapa, Cape Campbell, and Hawke’s Bay) and the west coast (Tasman Bay/Golden Bay and Upper West Coast of South Island). Allele frequencies from 55 loci were associated with at least one of six environmental variables, of which 47 correlated strongly with yearly mean water temperature. Although genes associated with these loci are linked to various functions, the most common functions were integral components of membrane and cilium assembly. Projection of the RDA indicates the existence of a latitudinal temperature cline. Our work provides the first genomic insights supporting panmixia of tarakihi in New Zealand and evidence of a genomic cline that appears to be driven by the temperature gradients, together providing crucial information to inform the stock assessment of this species, and to widen the insights of the ecological drivers of adaptive variation in a marine species.

Aquaculture is the fastest-growing food production sector worldwide, yet industry has been slow to implement genomic techniques as routine tools. Applying genomics to new breeding programmes can provide important information about pedigree structure and genetic diversity; key parameters for a successful long-term breeding programme. It can also provide insights on potential gains for commercially important, yet complex, quantitative traits such as growth rate. Here we investigated a population of 1100 captive-bred F-1 silver trevally (Pseudocaranx georgianus), a promising new species for New Zealand aquaculture. We used whole-genome information, coupled with image-based phenotypic data collected over two years, to build the pedigree of the population, assess its genetic diversity, describe growth patterns of ten growth traits and estimate their genetic parameters. Successful parentage assignment of 664 F-1 individuals showed that the pedigree consisted of a complex mixture of full- and half-sib individuals, with skewed reproductive success among parents, especially in females. Growth patterns showed seasonal fluctuations (average increase across all traits of 27.3% in summer and only 7% in winter) and strong inter-family differences. Heritability values for growth traits ranged from 0.27 to 0.76. Genetic and phenotypic correlations between traits were high and positive, ranging from 0.57 to 0.94 and 0.50 to 1.00 respectively. The implications of these findings are threefold: first, the best on-growing conditions are in warmer months, where highest growth peaks can be achieved; second, size- and family-based selection can be used as early selection criterion if pedigree structure and inbreeding risks are closely monitored; third, selection for body length results in concomitant increases in height and weight, traits of paramount importance for aquaculture. It is concluded that there is substantial potential for genetic improvement of economically important traits, suggesting that silver trevally is a promising species for selective breeding for enhanced growth.

Comparative analysis of whole-genome sequences can provide valuable insights into the evolutionary patterns of diversification and adaptation of species, including the genome contents and the regions under selection. However, such studies are lacking for fishes in New Zealand. To supplement the recently sequenced genome of tarakihi ( Nemadactylus macropterus ), the genomes of five additional percomorph species native to New Zealand (king tarakihi ( Nemadactylus n.sp.), blue moki ( Latridopsis ciliaris ), butterfish ( Odax pullus ), barracouta ( Thyrsites atun ), and kahawai ( Arripis trutta) ) were determined and assembled using Illumina sequencing. While the proportion of repeat elements was highly correlated with the genome size ( R 2 = 0.97, P < 0.01), most of the metrics for the genic features (e.g. number of exons or intron length) were significantly correlated with assembly contiguity (| R 2 | = 0.79–0.97). A phylogenomic tree including eight additional high-quality fish genomes was reconstructed from sequences of shared gene families. The radiation of Percomorpha was estimated to have occurred c. 112 mya (mid-Cretaceous), while the Latridae have diverged from true Perciformes c. 83 mya (late Cretaceous). Evidence of positive selection was found in 65 genes in tarakihi and 209 genes in Latridae: the largest portion of these are involved in the ATP binding pathway and the integral structure of membranes. These results and the de novo genome sequences can be used to (1) inform future studies on both the strength and shortcomings of scaffold-level assemblies for comparative genomics and (2) provide insights into the evolutionary patterns and processes of genome evolution in bony fishes.

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.

Tarakihi (Nemadactylus macropterus) is a demersal fish that supports valuable commercial, recreational, and customary fisheries in New Zealand. However, little is known about its stock structure. The population genetic structure, genetic diversity, and demographic history of N. macropterus were investigated using the hypervariable region one of the mitochondrial control region. 370 samples from 14 locations around New Zealand were collected. While weak genetic breaks were detected between Hawke’s Bay and East Northland and between the west and east coasts of South Island, no clear genetic structure was detected for the overall New Zealand area (ФST = 0.002, P = 0.18), indicative of a panmictic genetic structure. N. macropterus display a high level of genetic diversity and appear to have a historically large and stable population with a long evolutionary history. Bayesian skyline analysis indicates that the historic population has gone through two expansions, likely caused by repeated glacial cycles during the second half of the Pleistocene. The addition of 15 king tarakihi samples (Nemadactylus n.sp.) collected from the Three Kings Islands showed a clear genetic differentiation between the two morphotypes. These findings can inform the future management of N. macropterus and N. n.sp. to ensure a sustainable harvest.

Growth directly influences production rate and therefore is one of the most important and well-studied trait in animal breeding. However, understanding the genetic basis of growth has been hindered by its typically complex polygenic architecture. Here, we performed quantitative trait locus (QTL) mapping and genome-wide association studies (GWAS) for 10 growth traits that were observed over two years in 1,100 F 1 captive-bred trevally ( Pseudocaranx georgianus ). We constructed the first high-density linkage map for trevally, which included 19,861 single nucleotide polymorphism (SNP) markers, and discovered eight QTLs for height, length and weight on linkage groups 3, 14 and 18. Using GWAS, we further identified 113 SNP-trait associations, uncovering 10 genetic hot spots involved in growth. Two of the markers found in the GWAS co-located with the QTLs previously mentioned, demonstrating that combining QTL mapping and GWAS represents a powerful approach for the identification and validation of loci controlling complex traits. This is the first study of its kind for trevally. Our findings provide important insights into the genetic architecture of growth in this species and supply a basis for fine mapping QTLs, marker-assisted selection, and further detailed functional analysis of the genes underlying growth in trevally.

Ectotherm species, such as marine fishes, depend on environmental temperature to regulate their vital functions. In finfish aquaculture production, being able to predict physiological responses in growth and other economic traits to temperature is crucial to address challenges inherent in the selection of grow-out locations. This will become an even more significant issue under the various predicted future climate change scenarios. In this study, we used the marine teleost silver trevally (Pseudocaranx georgianus), a species currently being explored as a candidate for aquaculture in New Zealand, as a model to study plasticity in gene expression patterns and growth in response to different temperatures. Using a captive study population, temperature conditions were experimentally manipulated for 1 month to mimic seasonal extremes. Phenotypic differences in growth were measured in 400 individuals, and gene expression patterns of pituitary gland and liver were determined in a subset of 100 individuals. Results showed that growth increased 50% in the warmer compared with the colder condition, suggesting that temperature has a large impact on metabolic activities associated with growth. A total of 265,116,678 single-end RNA sequence reads were aligned to the trevally genome, and 28,416 transcript models were developed (27,887 of these had GenBank accessions, and 17,980 unique gene symbols). Further filtering reduced this set to 8597 gene models. 39 and 238 differentially expressed genes (DEGs) were found in the pituitary gland and the liver, respectively (|log(2)FC| > 0.26, p-value < 0.05). Of these, 6 DEGs showed a common expression pattern between both tissues, all involved in housekeeping functions. Temperature-modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signalling, previously shown to be important for temperature tolerance in other fish species. An interesting finding of this study was that genes linked to the reproductive system were up-regulated in both tissues in the high treatment, indicating the onset of sexual maturation. Few studies have investigated the thermal plasticity of the gene expression in the main organs of the somatotropic axis simultaneously. Our findings indicate that trevally exhibit substantial growth differences and predictable plastic regulatory responses to different temperature conditions. We identified a set of genes that provide a list of candidates for further investigations for selective breeding objectives and how populations may adapt to increasing temperatures.

The Growth Hormone (GH) gene of the marine teleost, the Australasian snapper (Chrysophrys auratus), was identified and characterised from the reference genome showing it was approximately 5,577 bp in length and consisted of six exons and five introns. Large polymorphic repeat regions were found in the first and third introns, and putative transcription factor binding sites were identified. Phylogenetic analysis of the GH genes of perciform fish showed largely conserved coding regions and highly variable non-coding regions among species. Despite some exon sequence variation and an amino acid deletion identified between C. auratus and its sister species Chrysophrys/Pagrus major, the amino acid sequences and putative secondary structures were largely conserved across the Sparidae. A population-level assessment of 99 samples caught at five separate coastal locations in New Zealand revealed six variable alleles at the intron 1 site of the C. auratus GH gene. A population genetic analysis suggested that C. auratus from the five sample locations were largely panmictic, with no evidence for departure from Hardy Weinberg Equilibrium, and have a high level of heterozygosity. Overall these results suggest that the GH gene is largely conserved across the coding regions, but some variability could be detected. This article is protected by copyright. All rights reserved.

The Buller’s albatross species complex is composed of two asynchronously breeding subspecies, the Northern Buller’s albatross (Thalassarche bulleri platei) and Southern Buller’s albatross (Thalassarche bulleri bulleri). The aim of this study was to test for genetic differentiation between Northern and Southern Buller’s albatross and to reassess genetic connectivity between these populations. Genotyping-by-Sequencing (GBS) was used to estimate gene flow and genome-wide divergence using 13 T. b. platei and 40 T. b. bulleri samples. The STACKS de novo and reference guided pipelines were used to call single nucleotide polymorphisms (SNPs) for three data sets: one each for Northern and Southern Buller’s and a third for both taxa together. The number of SNPs in each de novo data set was relatively consistent from 12,148 to 11,898 for Northern and Southern Buller’s albatross collections, respectively. A random subsample of 1000 SNPs from each of the two groups indicated that mean per-site nucleotide diversity and heterozygosity were slightly higher for Northern Buller’s albatross (π = 0.335; HE = 0.322) than for either of the two Southern Buller’s albatross breeding colonies (π = 0.286 and 0.294; HE = 0.275 and 0.288). Both STRUCTURE and discriminant analysis of principal components (DAPC) consistently showed differentiated clusters corresponding to Northern and Southern Buller’s but did not resolve population structure among Southern Buller’s breeding populations. These results indicate that an asynchronous breeding season likely limits gene flow between Northern and Southern Buller’s albatross and have important implications for the taxonomic status of Buller’s albatrosses.

Sustainable management of wild fisheries requires accurate delineation of reproductively isolated stocks to avoid depletion of a commercially and ecologically important resource. However, there is still a lack of reliable information on stock structure for most fishery species in New Zealand. DNA markers can assist in the delineation of stocks, but they also can provide significant insights into other areas related to the genetic diversity and the response to pressures. In this review, we first provide a detailed summary of the population genetic studies of New Zealand fish species, with a particular focus on hoki, orange roughy, snapper, ling, and blue cod. We find that genetic data is uniformly lacking for most species. We then discuss how the global shift from low resolution markers to genomics in fisheries genetics has far reaching consequences for the sustainable management of our aquatic resources, by allowing us to address multiple important pressures that wild fisheries are currently facing, and we introduce some of these briefly. We conclude by emphasising the need for a more systematic and holistic approach for the use of genomics in New Zealand fisheries management, so that the best evidence is available to inform the decisions of policy makers.

The genus Sprattus comprises five species of marine pelagic fishes distributed worldwide in antitropical, temperate waters. Their distribution suggests an ancient origin during a cold period of the earth’s history. In this study, we evaluated this hypothesis and corroborated the non-monophyly of the genus Sprattus , using a phylogenetic approach based on DNA sequences of five mitochondrial genome regions. Sprattus sprattus is more closely related to members of the genus Clupea than to other Sprattus species. We also investigated the historical biogeography of the genus, with the phylogenetic tree showing two well-supported clades corresponding to the species distribution in each hemisphere. Time-calibrated phylogenetic analyses showed that an ancient divergence between Northern and Southern Hemispheres occurred at 55.8 MYBP, followed by a diversification in the Oligocene epoch in the Northern Hemisphere clade (33.8 MYBP) and a more recent diversification in the Southern Hemisphere clade (34.2 MYBP). Historical biogeography analyses indicated that the most recent common ancestor (MRCA) likely inhabited the Atlantic Ocean in the Southern Hemisphere. These results suggest that the ancestral population of the MRCA diverged in two populations, one was dispersed to the Northern Hemisphere and the other across the Southern Hemisphere. Given that the Eocene was the warmest epoch since the Paleogene, the ancestral populations would have crossed the tropics through deeper cooler waters, as proposed by the isothermal submergence hypothesis. The non-monophyly confirmed for the genus Sprattus indicates that its systematics should be re-evaluated.