Biology subjects

Ritchie, P. A.

Publications and source records attributed to Ritchie, P. A..

7 recordsLinked to original sources

bioRxiv2026

Integrating genome-wide neutral and putatively adaptive variation resolves population structure and differentiation in a recently diverged albatross complex

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.

evolutionary biology↗

bioRxiv2022

Comparative genomics of tarakihi (Nemadactylus macropterus) and five New Zealand fish species: assembly contiguity affects the identification of genic features but not transposable elements

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 (R2 = 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 (| R2| = 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.

genomics↗

bioRxiv2022

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

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 (92x coverage) and 73 Gb of long Nanopore reads (122x) 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.

genomics↗

bioRxiv2022

Genomic stock structure of the marine teleost tarakihi (Nemadactylus macropterus) provides evidence of fine-scale adaptation and a temperature-associated cline amid panmixia

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 ([FE]ST < 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 Hawkes 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.

genomics↗

bioRxiv2021

Unravelling the complex genetic basis of growth in New Zealand silver trevally (Pseudocaranx georgianus)

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 F1 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.

genomics↗

bioRxiv2018

Domestication and temperature modulate gene expression signatures and growth in the Australasian snapper Chrysophrys auratus

ABSTRACT\n\nIdentifying genes and pathways involved in domestication is critical to understand how species change in response to human-induced selection pressures. We experimentally manipulated temperature conditions for F1-hatchery and wild Australasian snapper (Chrysophrys auratus) for 18 days and measured differences in growth, white muscle RNA transcription and haematological blood parameters. Over 2.2 Gb paired-end reads were assembled de novo for a total set of 33,017 transcripts (N50 = 2,804). We found pronounced growth and gene expression differences between wild and domesticated individuals related to global developmental and immune pathways. Temperature modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signalling. This study is the first step towards gaining an understanding of the changes occurring in the early stages of domestication, and the mechanisms underlying thermal adaptation and associated growth in poikilothermic vertebrates. Our study further provides the first transcriptome resources for studying biological questions in this non-model fish species.

evolutionary biology↗

bioRxiv2018

High-density linkage map and QTLs for growth in snapper (Chrysophrys auratus)

Characterizing the genetic variation underlying phenotypic traits is a central objective in biological research. This research has been hampered in the past by the limited genomic resources available for most non-model species. However, recent advances in sequencing technology and related genotyping methods are rapidly changing this. Here we report the use of genome-wide SNP data from the ecologically and commercially important marine fish species Chrysophrys auratus (snapper) to 1) construct the first linkage map for this species, 2) scan for growth QTLs, and 3) search for candidate genes in the surrounding QTL regions. The newly constructed linkage map contained ~11K SNP markers and is the densest map to date in the fish family Sparidae. Comparisons with available genome scaffolds indicated that overall marker placement was strongly correlated between the scaffolds and linkage map (R = 0.7), but at fine scales (< 5 cM) there were some precision limitations. Of the 24 linkage groups, which reflect the 24 chromosomes of this species, three were found to contain QTLs with genome-wide significance for growth-related traits. A scan for 13 known candidate growth genes located the genes for growth hormone, parvalbumin, and myogenin within 13.2, 2.6, and 5.0 cM of these genome-wide significant QTLs, respectively. The linkage map and QTLs found in this study will advance the investigation of genome structure and selective breeding in snapper.

evolutionary biology↗