Biology subjects

Larson, W.

Publications and source records attributed to Larson, W..

7 recordsLinked to original sources

bioRxiv2025

A case for multi-gear assessments: Detection probabilities of nearshore fish with eDNA and seine nets vary by functional traits

Ecological studies aim to understand species distributions, yet the methods used to sample affect which species are detected (i.e., gear selectivity) and may be influenced by species traits. Interactions between traditional gear selectivity for marine fishes and their species traits have been studied, but such studies have generally not extended to selectivity of environmental DNA (eDNA). Here, we investigated which functional species traits (scale type, schooling behaviour, and position-in-water-column) are selected for by eDNA metabarcoding and beach seines in nearshore eelgrass, mixed eelgrass, and understory kelp habitats. Using data from 35 sites across southeast Alaska, we applied occupancy modeling to estimate detection of species traits by each gear type. Detection probability with eDNA was 27 times greater for species with deciduous scales compared to species with non-deciduous scales, and lower for species with plates (rather than scales). Conversely, species with plates showed greater odds of detection with beach seines. Given the novelty of eDNA sampling, quantifying interactions between functional traits and gear selectivity will be important to accurately characterize species distributions across marine habitats.

ecology↗

bioRxiv2025

Phylogenetically diverse introgression drives subtle population structure in Pacific rockfishes

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 Americas 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.

evolutionary biology↗

bioRxiv2024

Genomic signals of local adaptation in Eleginops maclovinus from Northern Chilean Patagonia

Understanding the evolutionary mechanisms that shape the adaptive divergence across spatially heterogeneous environments is a challenging task for evolutionary ecologists. The Chilean marine Patagonia is a complex ecosystem with diverse geomorphology and physical-chemical oceanographic conditions. There is limited research evaluating the interactions between selective forces and environmental conditions in this area. This study focuses on identifying the genomic signals of local adaptation of the endemic marine fish, Eleginops maclovinus from Chilean North Patagonia. To achieve this goal, we used an environmental marine database (temperature, salinity, oxygen, phosphate nitrate and silicate concentration) with collected from 1995 to 2018 and 11,961 SNPs obtained from 246 individuals from 10 sampling locations across this area. We identified putative adaptive loci using ten bioinformatic software tools, where five were based on population genetic differentiation (PGD) and five based on the genotype-environment association (GEA). We identified 392 adaptative loci using PGD and 2,164 associated with at least one of the six environmental variables analyzed using GEA. A total of 131 loci were shared between the PGD and GEA approaches, of which 37 were associated with genes involved in the growth, metabolism and homeostasis. Then, we evaluated the variation of adaptive loci with environmental variables using polygenic scores and found significant correlations with temperature, salinity, and oxygen, indicating polygenic selection along environmental gradients. This study highlights how polygenic selection drives local adaptation in Eleginops maclovinus and underscores the value of integrating genomic and environmental data for conservation in the Patagonian ecosystem.

evolutionary biology↗

bioRxiv2024

A major effect locus involved in migration timing is shared by pink and sockeye salmon

AbstractWhole genome duplication (WGD) provides evolutionary opportunities to increase biological complexity and phenotypic diversity by selective retention of duplicated genes. We identify a small genomic region in salmon that governs complex life history variation and has diversified across four WGDs to fine-tune trait expression. Within this region, three large-effect loci on three chromosomes modulate migration timing across four species - a critical trait optimizing fitness by synchronizing reproduction and environmental conditions. Life history and genome resequencing data support intraspecific evolution of polymorphisms related to early- and late-reproducing phenotypes. We demonstrate that the repeated evolution of loci underlying reproductive timing carries the signature of WGD-facilitated adaptive evolution. This adaptation is driven by the subsequent subfunctionalization of genes within the highly conserved HPG axis, which regulates vertebrate reproduction.

genomics↗

bioRxiv2023

Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae

The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.

genomics↗

bioRxiv2022

Dispersive currents from narrow windows of time explain patterns of population connectivity in an ecologically and economically important fish

Identifying the drivers of population connectivity remains a fundamental question in ecology and evolution. Answering this question can be challenging in aquatic environments where dynamic lake and ocean currents, high variance in reproductive success, and above average rates of dispersal and gene flow can increase noise. We developed a novel, integrative approach that couples detailed biophysical models with eco-genetic individual-based models to generate predictive values of genetic differentiation. We also used RAD-Seq to genotype 960 yellow perch (Perca flavescens), a species with an [~]30-day pelagic larval duration (PLD), collected from 20 sites circumscribing Lake Michigan. By comparing predictive and empirical values of genetic differentiation, we estimated the relative contributions for known drivers of population connectivity (e.g., currents, behavior, PLD). For the main basin populations (i.e., the largest contiguous portion of the lake), we found that high gene flow led to low overall levels of genetic differentiation among populations (FST = 0.003). By far the best predictors of genetic differentiation were connectivity matrices that 1. came from a specific week and year, and 2. resulted in high population connectivity. Thus, these narrow windows of time during which highly dispersive currents occur are driving the patterns of population connectivity in this system. We also found that populations from the northern and southern main basin are slightly divergent from one another, while those from Green Bay and the main basin are highly divergent (FST = 0.11). By integrating biophysical and eco-genetic models with genome-wide data, we illustrate that the drivers of population connectivity can be identified in high gene flow systems.

ecology↗

bioRxiv2019

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

BackgroundYellow perch, Perca flavescens, is an ecologically and commercially important species native to a large portion of the northern United States and southern Canada. It is also a promising candidate species for aquaculture. No yellow perch reference genome, however, has been available to facilitate improvements in both fisheries and aquaculture management practices.\n\nFindingsBy combining Oxford Nanopore Technologies long-reads, 10X genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). Genome annotation identified 41.7% (366 Mb) of repeated elements and 24,486 genes including 16,579 genes (76.3%) significantly matching with proteins in public databases. We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping test which accurately differentiates XY genetic males (amhr2by+) from XX genetic females (amhr2by-).\n\nConclusionsOur high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries, and aquaculture research. In addition, the characterization of the amhr2by gene as a candidate sex determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

genomics↗