Biology subjects

Roach, J. L.

Publications and source records attributed to Roach, J. L..

3 recordsLinked to original sources

bioRxiv2025

Evidence of positive polygenic selection following a series of environmental and demographic disasters in Pacific herring

The causes and consequences of population collapse and recovery are difficult to discern and therefore predict because historical data are often sparse, and environmental drivers may interact in complex ways. Yet the influence of environmental change can imprint in contemporary and historic DNA sequences, thereby offering clues about drivers of population dynamics. The Prince William Sound (PWS) stock of Pacific herring famously collapsed in the early 1990s following the Exxon Valdez oil spill (EVOS), yet the causes of the collapse and reasons for a persistent lack of recovery are controversial. Three seasons after the spill, the PWS population declined precipitously, coincident with repeated disease outbreaks, and has remained small across the three decades since. We use population genetics as a forensic tool to gain insight into the causes and consequences of the collapse. We tracked genome-wide genetic variation across time, spanning the period immediately after the spill but preceding the collapse (1991) and across three subsequent decades to 2017. We compared genetic change through time between the PWS population and two reference Alaska populations. We detected high genetic differentiation between the Bering Sea and the Gulf of Alaska, and relatively small but significant genetic structure within the Gulf of Alaska. No loss of genome-wide genetic diversity was observed in the PWS population after the collapse. We did not detect any evidence for selective sweeps at individual loci. However, using sensitive temporal covariance methods, we detected significant signatures of positive polygenic adaptation in the PWS population but not in either of the reference populations. Gene functional enrichment analysis is consistent with selection acting on immune function and pathways that regulate crude oil developmental toxicity in the period following the spill and collapse. This suggests that environmental perturbations unique to the PWS region, including oil spills and disease outbreaks, affected the fitness of resident fish, and shifted their population genetic trajectory.

evolutionary biology↗

bioRxiv2023

Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect

The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts the influence of few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that a few large-effect QTL loci accounted for resistance to PCB- mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling, where some (but not all) of these QTL loci were shared across all populations, and some (but not all) of these loci showed signatures of recent natural selection in the corresponding wild population. Some strong candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.

evolutionary biology↗

bioRxiv2019

Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American killifish from the Fundulus genus

Draft de novo reference genome assemblies were obtained from four North American killifish species (Fundulus xenicus, Fundulus catenatus, Fundulus nottii, and Fundulus olivaceus) using sequence reads from Illumina and Oxford Nanopore Technologies PromethION platforms. For each species, the PromethION platform was used to generate 30-45x sequence coverage, and the Illumina platform was used to generate 50-160x sequence coverage. Contig N50 values ranged from 0.4 Mb to 2.7 Mb, and BUSCO scores were consistently above 90% complete using the Eukaryota database. Draft assemblies and raw sequencing data are available for public use. We encourage use and re-use of these data for assembly benchmarking and external analyses.

genomics↗