Biology subjects

Bemmels, J. B.

Publications and source records attributed to Bemmels, J. B..

5 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

Ancient transposable elements sustain global ecological adaptation despite chronically low nucleotide diversity

Transposable elements (TEs) are dynamic components of eukaryotic genomes and a major source of structural and regulatory variation, yet their contribution to ecological adaptation over evolutionary time remains unresolved. This uncertainty is particularly acute in species that occupy broad environmental niches despite chronically low nucleotide diversity, where conventional models predict limited adaptive potential. Here we show that ancient TE polymorphisms underpin global ecological adaptation in Spirodela polyrhiza, one of the smallest flowering plants with low genome-wide nucleotide diversity. Most TE polymorphisms predate continental population divergence. Cold-season temperature emerges as the dominant selective axis, with adaptive signals overwhelmingly associated with TE polymorphisms rather than SNPs. These adaptive TEs bear signatures of selection on standing variation and are embedded in genomic regions shaped by relaxed purifying selection rather than recent hard sweeps. Our results reveal how ancient TE variation sustains ecological adaptation despite chronically depleted nucleotide diversity, resolving a longstanding evolutionary paradox. One sentence summaryHow species adapt with little genetic diversity is a longstanding evolutionary puzzle solved by ancient transposon insertions

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↗

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↗

bioRxiv2017

Widespread southern forests during the Last Glacial Maximum, not refugia, explain genetic structure of two eastern North American hickory species

AimPhylogeographic studies of temperate forest taxa often infer complex histories involving population subdivision into distinct refugia during the Last Glacial Maximum (LGM). However, temperate forests may have been broadly distributed in southeastern North America during the LGM. We investigate genome-wide genetic structure in two widespread eastern North America tree species to determine if range expansion from a contiguous area or from genetically isolated refugia better explains the postglacial history of trees and forests from this region.\n\nLocationEastern North America (ENA).\n\nTaxaBitternut hickory (Carya cordiformis (Wangenh.) K.Koch) and shagbark hickory (Carya ovata (Mill.) K.Koch).\n\nMethodsGenetic diversity and differentiation indices were calculated from >1,000 nuclear SNP loci genotyped in ca. 180 individuals per species sampled across ENA. Genetic structure was investigated using principle component analysis and genetic clustering algorithms. As an additional tool for inference, areas of suitable habitat during the LGM were predicted using species distribution models (SDMs).\n\nResultsPopulations across all latitudes showed similar levels of genetic diversity. Most genetic variation was weakly differentiated across ENA, with the exception of an outlier population of Carya ovata in Texas. Genetic structure in each species exhibited an isolation-by-distance pattern. SDMs predicted high LGM habitat suitability over much of the southeastern United States.\n\nMain conclusionsBoth hickory species likely survived the LGM in a large region of continuous habitat and recolonized northern areas in a single expanding front that encountered few migration barriers. More complex scenarios, such as forest refugia, need not be invoked to explain genetic structure. The genetically distinct Texas population of Carya ovata could represent a separate glacial refugium, but other explanations are possible. Relative to that of other temperate forest regions, the phylogeographic history of ENA may have been exceptionally simple, involving a northward range shift but without well defined refugia.

evolutionary biology↗