Runyang Nicolas Lou

Understanding how habitat and life history traits contribute to population genetic structure is critical for evaluating conservation risks and identifying optimal management of wild populations. Species derived from adaptive radiations can provide a useful model for studying such patterns because the presence of some consistent traits allows for closer examination of attributes which differ. Here, we examine population structure in rockfishes (genera Sebastes and Sebastolobus ), a group of speciose, recently diverged marine fishes that exhibit a continuum of genetic structure, from cryptic species to putative genetic panmixia. In this study, we analyse low‐coverage whole genome resequencing data from nine rockfish species and identify four major types of genetic differentiation: cryptic diversity, isolation‐by‐distance (IBD), no detectable structure (putative panmixia) and no detectable structure with a single genomic region putatively underlying local adaptation. Two species, Dark ( Sebastes ciliatus ) and Northern ( S. polyspinis ) rockfishes, each exhibited cryptic diversity consisting of two sympatric groups differentiated at every chromosome throughout the genome. Black rockfish in Southeast Alaska also had two genetic groups, despite an overall signal of IBD from the West Coast of North America through the Gulf of Alaska (GOA). Five species showed evidence of genetic panmixia throughout the sampled range, while Yelloweye Rockfish exhibited high gene flow across ~4000 km, from southern California to the GOA, but had strong differentiation between the Salish Sea and the outer coast. Of the species in which no structure was detected, only Blackspotted Rockfish had one outlier region exhibiting signatures of potential local adaptation. Our results highlight how multiple mechanisms likely promote genetic structure in rockfishes, hinting at tentative links to depth distributions and offshore habitats that might influence patterns of differentiation in rockfishes more broadly. Further, this study provides genetic data for some of the most abundant rockfishes in commercial fisheries in the Northeast Pacific, enhancing the scientific information available for informing fisheries management.

Genomic methods have shown that admixture and introgression are common across animal taxa. Pacific rockfishes, genus Sebastes , are a group of commercially important species that primarily inhabit inshore, shelf and slope habitats along the North American west coast. Among these, Copper and Quillback Rockfishes are closely related species known to hybridize, particularly within the Salish Sea in North America's Pacific Northwest. Here, we investigate genetic population structure and introgression patterns in Copper and Quillback Rockfish from Alaska to California. Using whole‐genome resequencing across a broad geographic range, we seek to (1) compare population structure between these species, and (2) assess how introgression affects population structure patterns. Our analyses reveal that Copper exhibits much higher levels of population differentiation compared to Quillback, especially separating Salish Sea samples from all other populations. In contrast, Quillback populations appear to be nearly panmictic, with lower overall differentiation. Surprisingly, we detected signatures of introgression from seven other rockfish species in Copper and 10 species in Quillback. This introgression was highly regional, suggesting hybridization depended on geographic or environmental context. Yelloweye Rockfish introgression in the Salish Sea drives the strongest signal of regional population structure in Quillback. These findings provide novel insights into the range‐wide genetic structure of these species and highlight that hybridization in Sebastes is phylogenetically broader than previously appreciated.

Structural variants (SVs) contribute substantially to genetic variation and play vital roles in adaptation and disease ^1,2 . Nonetheless, SVs are poorly captured by short reads and thus remain understudied, especially in non-model organisms ^3,4 . Here, using haplotype-resolved genome assemblies from >600 vertebrate species, we comprehensively survey the landscape of SVs across >500 million years of evolution. We identify 35.3 million SVs and 3.12 billion single nucleotide variants (SNVs) segregating between two representative haplotypes across species, with SVs impacting ∼12-fold more base pairs. SV and SNV heterozygosity are correlated across species, with endangered and threatened species exhibiting reduced genetic diversity. However, the contribution of SVs relative to SNVs fundamentally differs across major vertebrate clades: given the same number of SNVs, fishes, amphibians, and reptiles have 4.3-to-9.1 times the number of SVs than birds, and 1.7-to-3.6 times more than mammals. This reduction in the relative contribution of SVs in mammals and birds is linked to fewer non-repeat-associated SVs as well as lower transposable element (TE) abundance and diversity. We identify features underlying genomic instability across vertebrates, finding that SVs frequently occur in repetitive and SNV-rich regions and are mediated by both homology and non-canonical DNA structures. Notably, G-quadruplex structures are enriched 11.5-fold around SV breakpoints in birds, while Z-DNA structures are enriched 2.2-fold in cartilaginous fishes. TEs uniquely contribute to SVs both directly through transposition and indirectly by mediating ectopic recombination, with the proportion of TE-mediated SVs influenced by both genomic TE density and diversity. We identify >10,000 instances of recent TE turnover including extinction of LINE-2 in therian mammals and slowing of CR1 activity in passerine birds. Finally, we show that SVs have an outsized role in functional genetic variation and are >70 times more likely to strongly impact protein-coding sequences than SNVs. While SVs are on average deleterious, we identify extensive recurrent structural variation across multiple taxa in genes involved in sensory, immune, and metabolic systems. Together, this study highlights extraordinary variation in the abundance, composition, mechanism, and functional impact of SVs across vertebrates.

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for ∼97% of vertebrate orders, along with additional lineages within those orders, totaling 815 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods, alongside the growth of associated consortium initiatives and international collaborations. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers the reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine.

Genomic methods have shown that admixture and introgression is common across animal taxa. Pacific rockfishes, genus Sebastes , are group of commercially important species that primarily inhabit inshore, shelf, and slope habitats along the North American west coast. Among these, Copper and Quillback Rockfishes (abbreviated to Copper and Quillback) are closely related species known to hybridize, particularly within the Salish Sea in North America’s Pacific Northwest. Here, we investigate genetic population structure and introgression patterns in Copper and Quillback from Alaska to California. Using whole-genome resequencing (WGS) across a broad geographic range, we seek to (1) compare population structure between these species, and (2) assess how introgression affects population structure patterns. Our analyses reveal that Copper exhibit much higher levels of population differentiation compared to Quillback, especially separating Salish Sea samples from all other populations. In contrast, Quillback populations appear to be nearly panmictic, with lower overall differentiation. Surprisingly, we detected signatures of introgression from 13 other rockfish species in Copper and 16 species in Quillback. This introgression was highly regional suggesting hybridization depended on geographic context and congener ranges. Yelloweye Rockfish introgression drives the strongest signal of regional population structure in Quillback. These findings provide novel insights into the range-wide genetic structure of these species and highlight that hybridization in Sebastes is phylogenetically broader than previously appreciated.

Ostrea edulis, the European flat oyster, was once a widespread economically and ecologically important marine species, but has suffered dramatic declines over the past two centuries. Consequently, there has been a surge in European restoration efforts, many of which focus on restocking as a conservation measure. In this study, we used whole‐genome sequencing (WGS) data to investigate the population structure, demographic history, and patterns of local adaptation of O. edulis across its natural distribution with increased sampling densities at Scandinavian localities. Results revealed seven distinct genetic clusters, including previously undescribed complex population structure in Norway, and evidence for introgression between genetic clusters in Scandinavia. We detected large structural variants (SVs) on three pseudo‐chromosomes. These megabase long regions were characterised by strong linkage disequilibrium and clear geographical differentiation, suggestive of chromosomal inversions potentially associated with local adaptation. The results indicated that genomic traces of past translocations of non‐native O. edulis were still present in some individuals, but overall, we found limited evidence of major impacts of translocations on the scale of contemporary population structure. Our findings highlight the importance of considering population structure and signatures of selection in the design of effective conservation strategies to preserve and restore wild native European flat oyster populations, and we provide direct knowledge safeguarding sustainable mitigation actions in this important species.

The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations¹. Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with high-starch intake², although evidence of recent selection is lacking^3,4. Here, using 94 long-read haplotype-resolved assemblies and short-read data from approximately 5,600 contemporary and ancient humans, we resolve the diversity and evolutionary history of structural variation at the amylase locus. We find that amylase genes have higher copy numbers in agricultural populations than in fishing, hunting and pastoral populations. We identify 28 distinct amylase structural architectures and demonstrate that nearly identical structures have arisen recurrently on different haplotype backgrounds throughout recent human history. AMY1 and AMY2A genes each underwent multiple duplication/deletion events with mutation rates up to more than 10,000-fold the single-nucleotide polymorphism mutation rate, whereas AMY2B gene duplications share a single origin. Using a pangenome-based approach, we infer structural haplotypes across thousands of humans identifying extensively duplicated haplotypes at higher frequency in modern agricultural populations. Leveraging 533 ancient human genomes, we find that duplication-containing haplotypes (with more gene copies than the ancestral haplotype) have rapidly increased in frequency over the past 12,000 years in West Eurasians, suggestive of positive selection. Together, our study highlights the potential effects of the agricultural revolution on human genomes and the importance of structural variation in human adaptation.

Summary: We developed loco-pipe, a Snakemake pipeline that seamlessly streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data. loco-pipe is highly automated, easily customizable, massively parallelized, and thus is a valuable tool for both new and experienced users of lcWGS. Availability and implementation: loco-pipe is published under the GPLv3. It is freely available on GitHub (github.com/sudmantlab/loco-pipe) and archived on Zenodo (doi.org/10.5281/zenodo.10425920).

Genomic methods are becoming increasingly valuable and established in ecological research, particularly in nonmodel species. Supporting their progress and adoption requires investment in resources that promote (i) reproducibility of genomic analyses, (ii) accessibility of learning tools and (iii) keeping pace with rapidly developing methods and principles. We introduce marineomics.io, an open‐source, living document to disseminate tutorials, reproducibility tools and best principles for ecological genomic research in marine and nonmodel systems. The website's existing content spans population and functional genomics, including current recommendations for whole‐genome sequencing, RAD‐seq, Pool‐seq and RNA‐seq. With the goal to facilitate the development of new, similar resources, we describe our process for aggregating and synthesizing methodological principles from the ecological genomics community to inform website content. We also detail steps for authorship and submission of new website content, as well as protocols for providing feedback and topic requests from the community. These web resources were constructed with guidance for doing rigorous, reproducible science. Collaboration and contributions to the website are encouraged from scientists of all skill sets and levels of expertise.

Over the past few decades, there has been an explosion in the amount of publicly available sequencing data. This opens new opportunities for combining data sets to achieve unprecedented sample sizes, spatial coverage or temporal replication in population genomic studies. However, a common concern is that nonbiological differences between data sets may generate patterns of variation in the data that can confound real biological patterns, a problem known as batch effects. In this paper, we compare two batches of low‐coverage whole genome sequencing (lcWGS) data generated from the same populations of Atlantic cod (Gadus morhua). First, we show that with a “batch‐effect‐naive” bioinformatic pipeline, batch effects systematically biased our genetic diversity estimates, population structure inference and selection scans. We then demonstrate that these batch effects resulted from multiple technical differences between our data sets, including the sequencing chemistry (four‐channel vs. two‐channel), sequencing run, read type (single‐end vs. paired‐end), read length (125 vs. 150 bp), DNA degradation level (degraded vs. well preserved) and sequencing depth (0.8× vs. 0.3× on average). Lastly, we illustrate that a set of simple bioinformatic strategies (such as different read trimming and single nucleotide polymorphism filtering) can be used to detect batch effects in our data and substantially mitigate their impact. We conclude that combining data sets remains a powerful approach as long as batch effects are explicitly accounted for. We focus on lcWGS data in this paper, which may be particularly vulnerable to certain causes of batch effects, but many of our conclusions also apply to other sequencing strategies.