Biology subjects

Owens, G. L.

Publications and source records attributed to Owens, G. L..

18 recordsLinked to original sources

bioRxiv2026

Genomic offsets predict observed kelp declines and suggest benefits of assisted migration in the Northeast Pacific

Kelp forests are widely distributed along temperate and polar coastlines worldwide and are among the worlds most productive and diverse marine ecosystems. Yet, due in part to ocean warming, they are declining and even disappearing in many parts of the world. While genomic tools can identify local adaptation and predict species responses to global change, these predictions have rarely been validated in the field, hampering their widespread use in conservation practice. Here, we applied a seascape genomics approach to investigate environmental adaptation in the two main canopy-forming species of the Northeast Pacific, Macrocystis tenuifolia and Nereocystis luetkeana. We leveraged whole-genome sequences of 598 individuals across 94 sites along the British Columbia and Washington coasts, together with 37 environmental variables. Both species showed genomic signatures of local adaptation, with distinct environmental drivers shaping adaptation in each species despite their co-occurrence across much of the studied area. Using gradient forests, we modelled the genetic turnover across environmental gradients and predicted populations vulnerability (genomic offset) under projected environmental conditions. Genomic offsets differed greatly among regions and were positively correlated with kelp declines observed to date, especially in Macrocystis, validating the link between genomic models and outcomes in the field and allowing us to translate genomic predictions into an ecologically meaningful metric: the risk of extirpation under global change. Our models predict that assisted migration could significantly attenuate kelps vulnerability to global change. Across environmentally heterogenous coastlines, short-distance migration can often substantially reduce future genomic-environmental mismatches, but in many cases, long-distance migration would be most beneficial. Our results highlight the potential of seascape genomics to predict vulnerability of populations to global change. Importantly, the validated link between our genomic models and ecological outcomes allows quantification of climate-driven extirpation risk and can inform conservation strategies to improve the resilience and sustainable management of these vulnerable ecosystems.

evolutionary biology↗

bioRxiv2026

Spatial inference of ancestor locations suggests northern refugia for canopy-forming kelps in the Northeast Pacific

O_LIPockets of the formerly glaciated Pacific coastline of North America likely remained ice-free throughout the Last Glacial Maximum (LGM). These areas may have served as refugia for terrestrial species, but less is known about their role in the persistence of coastal marine species. C_LIO_LIWe examined genetic diversity from >1,000 newly and previously sequenced whole genomes of canopy-forming kelps of the genera Nereocystis and Macrocystis, and built simple ecological niche models. We then reconstructed ancestral recombination graphs and modelled the geographic locations of genetic ancestors through time. C_LIO_LIWe detected high genetic diversity in both species in north-central British Columbia, in a region where suitable LGM habitat is plausible. Ancestor locations spatially converged backward in time toward this region, with multiple refugia inferred between northern Vancouver Island and southern Haida Gwaii. An expanded set of global samples for Macrocystis confirmed pre-LGM divergence with California but hinted at the possibility of subsequent gene flow. C_LIO_LIKelp forests survived in northern refugia and have continuously occupied portions of the northern Pacific coastline since the LGM. One implication of these results is their support for the Kelp Highway Hypothesis of the peopling of the Americas by a coastal route. C_LI

evolutionary biology↗

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

Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp

Kelp forests are declining in many parts of the northeast Pacific1-4. In small populations, genetic drift can reduce adaptive variation and increase fixation of recessive deleterious alleles5-7, but natural selection may purge harmful variants8-10. To understand evolutionary dynamics and inform restoration strategies, we investigated genetic structure and the outcomes of genetic drift and purging by sequencing the genomes of 429 bull kelp (Nereocystis luetkeana) and 211 giant kelp (Macrocystis pyrifera sensu lato11; cf. 12) from the coastlines of British Columbia and Washington. We identified 6-7 geographically and genetically distinct clusters in each species. Low effective population size was associated with low genetic diversity and high inbreeding coefficients (including increased selfing rates), with extreme variation in these genetic health indices among bull kelp populations but more moderate variation in giant kelp. We found no evidence that natural selection is purging putative recessive deleterious alleles in either species. Instead, genetic drift has fixed many such alleles in small populations of bull kelp, leading us to predict (1) reduced within-population inbreeding depression in small populations, which may be associated with an observed shift toward increased selfing rate, and (2) hybrid vigour in crosses between small populations. Our genomic findings imply several strategies for optimal sourcing and crossing of populations for restoration and aquaculture, but which require experimental validation. Overall, our work reveals strong genetic structure and suggests that conservation strategies should consider the multiple health risks faced by small populations whose evolutionary dynamics are dominated by genetic drift.

evolutionary biology↗

bioRxiv2024

Shared selection and genetic architecture drive strikingly repeatable evolution in long-term experimental hybrid populations

The degree to which evolution repeats itself has implications regarding the major forces driving evolution and the potential for evolutionary biology to be a predictive (versus solely historical) science. To understand the factors that control evolutionary repeatability, we experimentally evolved four replicate hybrid populations of sunflowers at natural sites for up to 14 years and tracked ancestry across the genome. We found that there was very strong negative selection against introgressed ancestry in several chromosomes, but positive selection for introgressed ancestry in one chromosome. Further, the strength of selection was influenced by recombination rate. High recombination regions had lower selection against introgressed ancestry due to more frequent recombination away from incompatible backgrounds. Strikingly, evolution was highly parallel across replicates, with shared selection driving 88% of variance in introgressed allele frequency change. Parallel evolution was driven by both high levels of sustained linkage in introgressed alleles and strong selection on large-effect quantitative trait loci. This work highlights the repeatability of evolution through hybridization and confirms the central roles that natural selection, genomic architecture, and recombination play in the process.

evolutionary biology↗

bioRxiv2023

Rapid turnover and evolution of sex-determining regions among Sebastes rockfishes

Nature has evolved a wealth of sex determination (SD) mechanisms, driven by both genetic and environmental factors. Recent studies of SD in fishes have shown that not all taxa fit the classic paradigm of sex chromosome evolution and diverse SD methods can be found even among closely related species. Here, we apply a suite of genomic approaches to investigate sex-biased genomic variation in eight species of Sebastes rockfish found in the northeast Pacific Ocean. Using recently assembled chromosome-level rockfish genomes, we leverage published sequence data to identify disparate sex chromosomes and sex-biased loci in five species. We identify two putative male sex chromosomes in S. diaconus, a single putative sex chromosome in the sibling species S. carnatus and S. chrysomelas, and an unplaced sex determining contig in the sibling species S. miniatus and S. crocotulus. Our study provides evidence for disparate means of sex determination within a recently diverged set of species, and sheds light on the diverse origins of sex determination mechanisms present in the animal kingdom.

evolutionary biology↗

bioRxiv2022

Re-evaluating homoploid reticulate evolution in the annual sunflowers.

Sunflowers of the genus Helianthus are models for hybridization research and contain three of the best studied examples of homoploid hybrid speciation. To understand the broader picture of hybridization within the annual sunflowers, we used whole genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find that all annual sunflower species tested have evidence of admixture, suggesting hybridization was common during the radiation of the genus. Support for the major species tree decreases with recombination rate, consistent with hybridization and introgression contributing to discordant topologies. Admixture graphs found hybridization to be associated with the origins of the three putative hybrid species (H. anomalus, H. deserticola, and H. paradoxus). However, the hybridization events are more ancient than suggested by previous work. Furthermore, H. anomalus and H. deserticola appear to have arisen from a single hybridization event involving an unexpected donor, rather than through multiple independent events as previously proposed. Using a broader data set that covers the whole Helianthus genus, including perennial species, we find that signals of introgression span the genus and beyond, suggesting highly divergent introgression and/or the sorting of ancient haplotypes. Thus, Helianthus can be viewed as a syngameon in which largely reproductively isolated species are linked together by occasional or frequent gene flow.

evolutionary biology↗

bioRxiv2022

The rate of inversion fixation in plant genomes is highly variable.

AO_SCPLOWBSTRACTC_SCPLOWChromosomal inversions are theorized to play an important role in adaptation by preventing recombination, but testing this hypothesis requires an understanding of the rate of inversion fixation. Here we use chromosome-level whole genome assemblies for 32 genera of plants to ask how fast inversions accumulate and what factors affect this rate. We find that on average species accumulate 4 to 28 inversions per million generations, but this rate is highly variable, and we find no correlation between sequence divergence or repeat content and the number of inversions and only a small correlation with chromosome size. We also find that inversion regions are depleted for genes and enriched for TEs compared to the genomic background. This suggests that idiosyncratic forces, like natural selection and demography, are controlling how fast inversions fix.

evolutionary biology↗

bioRxiv2022

The genomics of linkage drag in sunflower

Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here we comprehensively analyzed the genomic and phenotypic impacts of wild introgressions into cultivated sunflower to estimate the impacts of linkage drag. First, we generated new reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge regression model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including > 3,000 new genes. While introgressions reduced genetic load at protein-coding sequences and positively affected traits associated with abiotic stress resistance, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, pre-breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.

genomics↗

bioRxiv2022

Uncovering the hologenomic basis of an extraordinary plant invasion

While invasive species are a key driver of the global biodiversity crisis, the drivers of invasiveness remain debated. To investigate the genomic basis of invasiveness in plants, we use the invasive weed Ambrosia artemisiifolia, introduced to Europe in the late 19th century, resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In introduced European populations, we report selection signatures in defense genes and lower prevalence of particular plant pathogens in the invasive range. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from microbial enemies likely favoured the plants remarkable success as an invasive species. One-Sentence SummaryThe invasive success of European ragweed was facilitated by release from enemy microbes and inter-species hybridization.

genomics↗

bioRxiv2022

High homozygosity of inversions in sunflower species largely averts accumulation of deleterious mutations

Recombination is critical both for accelerating adaptation and for the purging of deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination and, thus, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance and coding sequence evolution across the genomes of 1,445 individuals from three sunflower species, as well as within nine inversions segregating within species. We also analyzed the effects of inversion genotypes on 87 phenotypic traits to test for overdominance. We found significant negative correlations of long terminal repeat retrotransposon abundance and deleterious mutations with recombination rates across the genome in all three species. However, we failed to detect an increase in these features in the inversions, except for a modest increase in the proportion of stop codon mutations in several very large or rare inversions. Moreover, there was little evidence of phenotypic overdominance in inversion heterozygotes, consistent with observations of minimal deleterious load. On the other hand, significantly greater load was observed for inversions in populations polymorphic for a given inversion compared to populations monomorphic for one of the arrangements, suggesting that the local state of inversion polymorphism affects deleterious load. These seemingly contradictory results can be explained by the geographic structuring and consequent excess homozygosity of inversions in wild sunflowers. Inversions contributing to local adaptation often exhibit geographic structure; such inversions represent ideal recombination modifiers, acting to facilitate adaptive divergence with gene flow, while largely averting the accumulation of deleterious mutations due to recombination suppression.

evolutionary biology↗

bioRxiv2021

Genetic basis and dual adaptive role of floral pigmentation in sunflowers

Variation in floral displays, both between and within species, has been long known to be shaped by the mutualistic interactions that plants establish with their pollinators. However, increasing evidence suggests that abiotic selection pressures influence floral diversity as well. Here we analyze the genetic and environmental factors that underlie patterns of floral pigmentation in wild sunflowers. While sunflower inflorescences appear invariably yellow to the human eye, they display extreme diversity for patterns of ultraviolet pigmentation, which are visible to most pollinators. We show that this diversity is largely controlled by cis-regulatory variation at a single MYB transcription factor, HaMYB111, through accumulation of UV-absorbing flavonol glycosides. As expected, different patterns of ultraviolet pigments in flowers have a strong effect on pollinator preferences. However, variation for floral ultraviolet patterns is also associated with environmental variables, especially relative humidity, across populations of wild sunflowers. Larger ultraviolet patterns, which are found in drier environments, limit transpiration, therefore reducing water loss. The dual role of floral UV patterns in pollination attraction and abiotic responses reveals the complex adaptive balance underlying the evolution of floral traits.

evolutionary biology↗

bioRxiv2021

Parallel shifts of visual sensitivity and body colouration in replicate populations of extremophile fish.

Visual sensitivity and body pigmentation are often shaped by both natural selection from the environment and sexual selection from mate choice. One way of quantifying the impact of the environment is by measuring how traits have changed after colonization of a novel habitat. To do this, we studied Poecilia mexicana populations that have repeatedly adapted to extreme sulphidic (H2S containing) environments. We measured visual sensitivity using opsin gene expression, as well as body pigmentation and water transmission for populations in four independent drainages. Both visual sensitivity and body pigmentation showed significant parallel shifts towards greater medium wavelength sensitivity and reflectance in sulphidic populations. The light spectrum was only subtly different between environments and overall, we found no significant correlations between the light environment and visual sensitivity or body pigmentation. Altogether we found that sulphidic habitats select for differences in visual sensitivity and pigmentation; our data suggest that this effect is unlikely to be driven purely by the waters spectral properties and may instead be from other correlated ecological changes.

evolutionary biology↗

bioRxiv2020

An unexpected donor in the adaptive introgression candidate Helianthus annuus subsp. texanus.

Hybridization is widely acknowledged as an important mechanism of acquiring adaptive variation. In Texas, the sunflower Helianthus annuus subsp. texanus is thought to have acquired herbivore resistance and morphological traits via introgression from a local congener, H. debilis. Here we test this hypothesis using whole genome sequencing data from across the entire range of H. annuus and possible donor species, as well as phenotypic data from a common garden study. We find that although it is morphologically convergent with H. debilis, H. a. texanus has conflicting signals of introgression. Genome wide tests (Pattersons D and TreeMix) only find evidence of introgression from H. argophyllus (sister species to H. annuus and also sympatric), but not H. debilis, with the exception of one individual of 109 analysed. We further scanned the genome for localized signals of introgression using PCAdmix and found minimal but non-zero introgression from H. debilis and significant introgression from H. argophyllus. Putative introgressions mainly occur in high recombination regions as predicted by theory if introgressed ancestry contains maladaptive alleles. To reconcile the disparate findings of our analyses, we discuss potential test-specific confounding features, including introgression from other taxa. Given the paucity of introgression from H. debilis, we argue that the morphological convergence observed in Texas is likely independent of introgression.

evolutionary biology↗

bioRxiv2019

Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype

Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencing data and newly developed population genomic approaches to identify putative inversions that differentiate a sand dune ecotype of the prairie sunflower (Helianthus petiolaris) from populations found on the adjacent sand sheet. We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and non-dune populations. These regions also show high linkage disequilibrium and high heterozygosity between, but not within haplotypes, consistent with the behavior of large inversions, an inference subsequently validated in part by comparative genetic mapping. Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions. The inversions co-locate with previously described \"islands of differentiation,\" and appear to play an important role in adaptive divergence and incipient speciation within H. petiolaris.

evolutionary biology↗

bioRxiv2019

Massive haplotypes underlie ecotypic differentiation in sunflowers

Species often include multiple ecotypes that are adapted to different environments. But how do ecotypes arise, and how are their distinctive combinations of adaptive alleles maintained despite hybridization with non-adapted populations? Re-sequencing of 1506 wild sunflowers from three species identified 37 large (1-100 Mbp), non-recombining haplotype blocks associated with numerous ecologically relevant traits, and soil and climate characteristics. Limited recombination in these regions keeps adaptive alleles together, and we find that they differentiate several sunflower ecotypes; for example, they control a 77 day difference in flowering between ecotypes of silverleaf sunflower (likely through deletion of a FLOWERING LOCUS T homolog), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, associated with polymorphic structural variants, and often appear to represent introgressions from other, possibly extinct, congeners. This work highlights a pervasive role of structural variation in maintaining complex ecotypic adaptation.

evolutionary biology↗

bioRxiv2019

Adaptive introgression during environmental change can weaken reproductive isolation

Anthropogenic climate change is an urgent threat to species diversity. One aspect of this threat is the collapse of species reproductive barriers through increased hybridization. The primary mechanism for this collapse is thought to be the weakening of ecologically-mediated reproductive barriers, as demonstrated in many cases of "reverse speciation" . Here, we expand on this idea and show that adaptive introgression between species adapting to a shared, moving climatic optimum can readily weaken any reproductive barrier, including those that are completely independent of the climatic variable. Using genetically explicit forward-time simulations, we show that genetic linkage between alleles conferring adaptation to a changing climate and alleles conferring reproductive isolation can lead to adaptive introgression facilitating the homogenization of reproductive isolation alleles. This effect causes the decay of species boundaries across a broad and biologically-realistic parameter space. We explore how the magnitude of this effect depends upon the rate of climate change, the genetic architecture of adaptation, the initial degree of reproductive isolation and the mutation rate. These results highlight a previously unexplored effect of rapid climate change on species diversity.

evolutionary biology↗

bioRxiv2017

A Novel Post Hoc Method For Detecting Index Switching Finds No Evidence For Increased Switching On The Illumina HiSeq X

High throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that index switching, where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in-progress work across the field. Here, we test for evidence of index switching in an exemplar whole genome shotgun dataset sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may. We leverage unbalanced heterozygotes, which may be produced by index switching, and ask whether the under-sequenced allele is more likely to be found in other samples in the same lane than expected based on the allele frequency. Although we validate the sensitivity of this method using simulations, we find that neither the HiSeq 2500 nor the HiSeq X have evidence of index switching. This suggests that, thankfully, index switching may not be a ubiquitous problem in HiSeq X sequence data. Lastly, we provide scripts for applying our method so that index switching can be tested for in other datasets.

bioinformatics↗