Department of Forest Resources and Environmental Conservation Recombination rate variation, hitchhiking, and central-peripheral structure shape deleterious load in black cottonwood Jason Holliday Department of Forest Resources and Environmental Conservation Virginia Tech

Understanding the adaptive past to predict the adaptive future The rate of adaptation to anthropogenic climate change depends on: Number of loci involved Distribution of effect sizes Distribution of adaptive alleles in the genome New mutation vs standing variation Many non-adaptive processes also play a role: Historical demography (e.g., bottlenecks) Migration rate relative to selection Deleterious alleles

Populus trichocarpa as model to understand adaptive potential and constraint Compact (~480mb), sequenced genome Clonal propagation Wide latitudinal and altitudinal range = strong differentiation for adaptive traits High gene flow via wind polination = low background population structure Postglacial history = possbile adaptive constraint

Sampling and phenotyping 449 samples spanning the latitudinal and altitudinal range of the species Outgroups: P. tremula, P. tremuloides, P. deltoides Re-sequence most of the ‘gene space’ Sequence capture Replicated gardens in Virginia and British Columbia Phenotyped for growth, bud phenology, cold hardiness

Genotyping by sequence capture

Sequence capture recovers regions of interest in a mostly repeatable way

Coverage is tightly linked to bait locations

Genomic sampling ~ 2 million single nucleotide polymorphisms passed quality filters

Adaptation is not just about having the ‘right’ alleles; it’s also about not having the ‘wrong’ alleles Many tree species suffer substantial inbreeding depression, while hybrid vigor is common Likely due in part to accumulation of deleterious alleles Wang et al 2004

Deleterious alleles Coding SNPs often simply categorized as synonymous (same amino acid) or non-synonymous (different amino acid) But not all non-synonymous SNPs are equivalent ≠ Ala Gly Ala Cys

Factors that may govern accumulation of deleterious allele Genomic Recombination Hitchhiking Direct positive selection – are some of these alleles conditionally advantageous? Demographic Population history (bottlenecks, etc) Population size (efficiency of selection)

Sorting Intolerant From Tolerant (SIFT) Uses multiple alignments from related species to classify SNPs as tolerated or damaging Examples: If no amino acid substitution is found at that site, any non-syn change is deleterious If only hydrophobic residues found, changes to other amino acid classes deleterious No information about protein structure, but performs similarly to algorithms that account for this Advantage: can be used on just about any sequence, not just those with known structure information

Deleterious SNPs segregate at lower frequency than tolerated SNPs Derived allele frequency

Deleterious SNPs segregate at lower frequency than tolerated SNPs Percent Deleterious : tolerated ratio Derived allele frequency

Determinants of deleterious frequency: recombination More generally – recombination rate variation correlated with deleterious ratio

Determinants of deleterious frequency: hitchhiking iHS = measure of incomplete hitchhiking events Deleterious ratio higher in top 1% of iHS windows iHS higher for windows enriched for deleterious SNPs Signal of direct or linked selection?

Any evidence for direct selection? FST outliers identified across three sampling transects (two altitudinal and one latitudinal) Deleterious alleles underrepresented among FST outliers Suggests deleterious alleles mostly not direct targets of positive selection

Determinants of deleterious frequency: historical demography Like many northern species, poplar experienced bottlenecks associated with Pleistocene glaciation Increased drift in leading edge populations More generally, variation in Ne across the range may lead to differential efficiency of purifying selection

Determinants of deleterious frequency: historical demography

Why does this matter? Deleterious alleles affect fitness BC Garden VA Garden

Can we detect the signature of deleterious alleles at individual SNP loci? Sort of – deleterious alleles overrepresented among associated genes, but underrepresented among associated SNPs Low frequency deleterious alleles generating ‘synthetic’ associations?

Conclusions Deleterious alleles impact performance, and may explain some phenotypic associations for tolerated SNPs Accumulate as a result of recombination rate variation, hitchhiking, and demographic history More common in peripheral populations Response to selection may be weaker in these populations, which suggests less adaptive potential under climate change

Acknowledgements Mandy Zhang, Lecong Zhou, Haktan Suren, Rajesh Bawa Kyle Peer, Clay Sawyers, Debbie Byrd (VA Garden) Mike Carlson (BC Forest Service) and Cees Van Oosten (BC Garden) Carl Douglas and BC Forest Service – access to some BC samples