From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles

The northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations to highly heterogeneous environments. Adult barnacles may be exposed to highly dissimilar levels of thermal stress depending on where they settle in the intertidal (i.e., closer to the upper or lower tidal boundary). For instance, barnacles near the upper tidal limit experience episodic summer temperatures above recorded heat coma levels. This differential stress at the microhabitat level is also dependent on the aspect of sun exposure. In the present study, we used pool-seq approaches to conduct a genome wide screen for loci responding to intertidal zonation across the North Atlantic basin (Maine, Rhode Island, and Norway). Our analysis discovered 382 genomic regions containing SNPs which are consistently zonated (i.e., SNPs whose frequencies vary depending on their position in the rocky intertidal) across all surveyed habitats. Notably, most zonated SNPs are young and private to the North Atlantic. These regions show high levels of genetic differentiation across ecologically extreme microhabitats concomitant with elevated levels of genetic variation and Tajima's D, suggesting the action of non-neutral processes. Overall, these findings support the hypothesis that spatially heterogeneous selection is a general and repeatable feature for this species, and that natural selection can maintain functional genetic variation in heterogeneous environments.publishedVersio

Supplementa data for: Population genomics and biogeography of the northern acorn barnacle (Semibalanus balanoides) using pooled-sequencing approaches

Supplemental material for Population genomics and biogeography of the northern acorn barnacle (Semibalanus balanoides) using pooled-sequencing approaches. The gene feature file (GFF, v3) of Sbal2 from the Drosophila AUGUSTUS model, the UniProt blast hits file, and the nuDNA and mtDNA tables are found here. The SNP tables are accompanied by a header description file

Transatlantic population genomics of the northern acorn barnacle (Semibalanus balanoides): a comparison of Fst outliers using different reference assemblies

A poster presented in the 2016 Evolution meeting at Austin, Texas. June 17 -23, 2016.<div><br></div><div>Works Cited in this poster:</div><div><br></div><div><div>[1] – Langmead, B. Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics Chapter 11, Unit 11 7 (2010).</div><div>[2] – Flight, P.A. & Rand, D.M. Genetic variation in the acorn barnacle from allozymes to population genomics. Integr Comp Biol 52, 418-29 (2012).</div><div>[3] – Safonova, Y., Bankevich, A. & Pevzner, P.A. dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. J Comput Biol 22, 528-45 (2015).</div><div>[4] –  arXiv:1410.2801 [q-bio.GN]</div><div>[5] – Berlin K, Koren S, Chin CS, Drake PJ, Landolin JM, Phillippy AM Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing. Nature Biotechnology. (2015).</div><div>[6] – A.F., Kann, L.M. & Rand, D.M. Gene flow versus local adaptation in the northern acorn barnacle, Semibalanus balanoides: insights from mitochondrial DNA variation. Evolution 55, 1972-9 (2001).</div><div>[7] – Kolaczkowski, B., Kern, A.D., Holloway, A.K. & Begun, D.J. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics 187, 245-60 (2011).</div><div><br></div><div>Additional Citations:</div><div>The FLK test was conducted as described in Bonhomme, M. et al. Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended. Genetics (2010).</div><div>Most analysis were conducted in PoPoolation and PoPoolation2 by: Kofler R, et al. (2011) PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals. PLoS ONE, and Kofler,R.,Vinay Pandey, R. & Schloetterer, C PoPoolation2: Identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq); Bioinformatics; Vol. 27 no. 24 2011, pages 3435–3436, respectively. </div><div> </div></div

From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles

The northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations to highly heterogeneous environments. Adult barnacles may be exposed to highly dissimilar levels of thermal stress depending on where they settle in the intertidal (i.e., closer to the upper or lower tidal boundary). For instance, barnacles near the upper tidal limit experience episodic summer temperatures above recorded heat coma levels. This differential stress at the microhabitat level is also dependent on the aspect of sun exposure. In the present study, we used pool-seq approaches to conduct a genome wide screen for loci responding to intertidal zonation across the North Atlantic basin (Maine, Rhode Island, and Norway). Our analysis discovered 382 genomic regions containing SNPs which are consistently zonated (i.e., SNPs whose frequencies vary depending on their position in the rocky intertidal) across all surveyed habitats. Notably, most zonated SNPs are young and private to the North Atlantic. These regions show high levels of genetic differentiation across ecologically extreme microhabitats concomitant with elevated levels of genetic variation and Tajima's D, suggesting the action of non-neutral processes. Overall, these findings support the hypothesis that spatially heterogeneous selection is a general and repeatable feature for this species, and that natural selection can maintain functional genetic variation in heterogeneous environments

Ecological load and balancing selection in circumboreal barnacles

AbstractAcorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question of how adaptation to high environmental variability is maintained in the face of strong juvenile dispersal and mortality. Here we show that 4% of genes in the barnacle genome experience balancing selection across the entire range of the species. Many of these genes harbor mutations maintained across 2 million years of evolution between the Pacific and Atlantic oceans. These genes are involved in ion regulation, pain reception, and heat tolerance, functions which are essential in highly variable ecosystems. The data also reveal complex population structure within and between basins, driven by the trans-Arctic interchange and the last glaciation. Divergence between Atlantic and Pacific populations is high, foreshadowing the onset of allopatric speciation, and suggesting that balancing selection is strong enough to maintain functional variation for millions of years in the face of complex demography.</jats:p

Ecological load and balancing selection in circumboreal barnacles

Acorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question of how adaptation to high environmental variability is maintained in the face of strong juvenile dispersal and mortality. Here, we show that 4% of genes in the barnacle genome experience balancing selection across the entire range of the species. Many of these genes harbor mutations maintained across 2 My of evolution between the Pacific and Atlantic oceans. These genes are involved in ion regulation, pain reception, and heat tolerance, functions which are essential in highly variable ecosystems. The data also reveal complex population structure within and between basins, driven by the trans-Arctic interchange and the last glaciation. Divergence between Atlantic and Pacific populations is high, foreshadowing the onset of allopatric speciation, and suggesting that balancing selection is strong enough to maintain functional variation for millions of years in the face of complex demography

T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

AbstractMeasuring the adaptive immune response to SARS-CoV-2 can enable the assessment of past infection as well as protective immunity and the risk of reinfection. While neutralizing antibody (nAb) titers are one measure of protection, such assays are challenging to perform at a large scale and the longevity of the SARS-CoV-2 nAb response is not fully understood. Here, we apply a T-cell receptor (TCR) sequencing assay that can be performed on a small volume standard blood sample to assess the adaptive T-cell response to SARS-CoV-2 infection. Samples were collected from a cohort of 302 individuals recovered from COVID-19 up to 6 months after infection. Previously published findings in this cohort showed that two commercially available SARS-CoV-2 serologic assays correlate well with nAb testing. We demonstrate that the magnitude of the SARS-CoV-2-specific T-cell response strongly correlates with nAb titer, as well as clinical indicators of disease severity including hospitalization, fever, or difficulty breathing. While the depth and breadth of the T-cell response declines during convalescence, the T-cell signal remains well above background with high sensitivity up to at least 6 months following initial infection. Compared to serology tests detecting binding antibodies to SARS-CoV-2 spike and nucleoprotein, the overall sensitivity of the TCR-based assay across the entire cohort and all timepoints was approximately 5% greater for identifying prior SARS-CoV-2 infection. Notably, the improved performance of T-cell testing compared to serology was most apparent in recovered individuals who were not hospitalized and were sampled beyond 150 days of their initial illness, suggesting that antibody testing may have reduced sensitivity in individuals who experienced less severe COVID-19 illness and at later timepoints. Finally, T-cell testing was able to identify SARS-CoV-2 infection in 68% (55/81) of convalescent samples having nAb titers below the lower limit of detection, as well as 37% (13/35) of samples testing negative by all three antibody assays. These results demonstrate the utility of a TCR-based assay as a scalable, reliable measure of past SARS-CoV-2 infection across a spectrum of disease severity. Additionally, the TCR repertoire may be useful as a surrogate for protective immunity with additive clinical value beyond serologic or nAb testing methods.</jats:p