@article{napier_grabowski_lovell_bonnette_mamidi_gomez-hughes_vanwallendael_weng_handley_kim_et al._2022, title={A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range}, volume={119}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85127497080&partnerID=MN8TOARS}, DOI={10.1073/pnas.2118879119}, abstractNote={Polyploidy results from whole-genome duplication and is a unique form of heritable variation with pronounced evolutionary implications. Different ploidy levels, or cytotypes, can exist within a single species, and such systems provide an opportunity to assess how ploidy variation alters phenotypic novelty, adaptability, and fitness, which can, in turn, drive the development of unique ecological niches that promote the coexistence of multiple cytotypes. Switchgrass, Panicum virgatum, is a widespread, perennial C4 grass in North America with multiple naturally occurring cytotypes, primarily tetraploids (4×) and octoploids (8×). Using a combination of genomic, quantitative genetic, landscape, and niche modeling approaches, we detect divergent levels of genetic admixture, evidence of niche differentiation, and differential environmental sensitivity between switchgrass cytotypes. Taken together, these findings support a generalist (8×)–specialist (4×) trade-off. Our results indicate that the 8× represent a unique combination of genetic variation that has allowed the expansion of switchgrass’ ecological niche and thus putatively represents a valuable breeding resource.}, number={15}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Napier, J.D. and Grabowski, P.P. and Lovell, J.T. and Bonnette, J. and Mamidi, S. and Gomez-Hughes, M.J. and VanWallendael, A. and Weng, X. and Handley, L.H. and Kim, M.K. and et al.}, year={2022} }
 @article{vanwallendael_alvarez_2022, title={Alignment-free methods for polyploid genomes: Quick and reliable genetic distance estimation}, volume={22}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85114920393&partnerID=MN8TOARS}, DOI={10.1111/1755-0998.13499}, abstractNote={Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic data sets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated haploid and polyploid short-read sequences with various levels of missing data. Mash-based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyse publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems or those with only poor-quality sequence data available.}, number={2}, journal={Molecular Ecology Resources}, author={VanWallendael, A. and Alvarez, M.}, year={2022}, pages={612–622} }
 @article{global urban environmental change drives adaptation in white clover_2022, volume={375}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85126689688&partnerID=MN8TOARS}, DOI={10.1126/science.abk0989}, abstractNote={Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.}, number={6586}, journal={Science}, year={2022}, pages={1275–1281} }
 @article{vanwallendael_lowry_hamilton_2022, title={One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems}, volume={66}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85123068407&partnerID=MN8TOARS}, DOI={10.1016/j.pbi.2021.102152}, abstractNote={A hundred years after Turesson first clearly described how locally adaptive variation is distributed within species, plant biologists are making major breakthroughs in our understanding of mechanisms underlying adaptation from local populations to the scale of continents. Although the genetics of local adaptation has typically been studied in smaller reciprocal transplant experiments, it is now being evaluated with whole genomes in large-scale networks of common garden experiments with perennial switchgrass and poplar trees. These studies support the hypothesis that a complex combination of loci, both with and without adaptive trade-offs, underlies local adaptation and that hybridization and adaptive introgression play a key role in the evolution of these species. Future studies incorporating high-throughput phenotyping, gene expression, and modeling will be used to predict responses of these species to climate change.}, journal={Current Opinion in Plant Biology}, author={VanWallendael, A. and Lowry, D.B. and Hamilton, J.A.}, year={2022} }
 @article{vanwallendael_benucci_costa_fraser_sreedasyam_fritschi_juenger_lovell_bonito_lowry_2021, title={Host genetic control of succession in the switchgrass leaf fungal microbiome}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85119534631&partnerID=MN8TOARS}, DOI={10.1101/2021.03.26.437207}, abstractNote={Abstract Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass ( Panicum virgatum ). We also sampled a replicated subset of genotypes across three additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association mapping and RNA-sequencing to show that three cysteine-rich receptor-like kinases were linked to a genetic locus associated with microbiome structure. These genes were more highly expressed in genotypes susceptible to fungal pathogens, which were central to microbial covariance networks, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.}, journal={bioRxiv}, author={VanWallendael, A. and Benucci, G.M.N. and Costa, P.B. and Fraser, L. and Sreedasyam, A. and Fritschi, F. and Juenger, T.E. and Lovell, J.T. and Bonito, G. and Lowry, D.B.}, year={2021} }
 @article{vanwallendael_alvarez_franks_2021, title={Patterns of population genomic diversity in the invasive Japanese knotweed species complex}, volume={108}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85105033095&partnerID=MN8TOARS}, DOI={10.1002/ajb2.1653}, abstractNote={PREMISE Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed ( Reynoutria japonica ), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity. METHODS We used genotyping by sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used alignment‐free k ‐mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids. RESULTS Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, giant knotweed, and hybrid bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, giant knotweed and hybrids showed distinct population groups. We did not find evidence of isolation by distance in the species complex, likely reflecting the stochastic introduction history of this species complex. CONCLUSIONS The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.}, number={5}, journal={American Journal of Botany}, author={VanWallendael, A. and Alvarez, M. and Franks, S.J.}, year={2021}, pages={857–868} }
 @article{vanwallendael_alvarez_2020, title={Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85098910245&partnerID=MN8TOARS}, DOI={10.1101/2020.10.23.352963}, abstractNote={Abstract Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash , a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic datasets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated diploid and polyploid short-read sequences with various levels of missing data. Mash- based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyze publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems with poor quality DNA.}, journal={bioRxiv}, author={VanWallendael, A. and Alvarez, M.}, year={2020} }
 @article{vanwallendael_bonnette_juenger_fritschi_fay_mitchell_lloyd-reilley_rouquette_bergstrom_lowry_2020, title={Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)}, volume={227}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85083783253&partnerID=MN8TOARS}, DOI={10.1111/nph.16555}, abstractNote={Summary Local adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described. To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust ( Puccinia spp.) severity in switchgrass ( Panicum virgatum ) plantings at eight locations across the central USA for 3 yr and conducted quantitative trait locus (QTL) mapping for rust progression. We mapped several variable QTLs, but two large‐effect QTLs which we have named Prr1 and Prr2 were consistently associated with rust severity in multiple sites and years, particularly in northern sites. By contrast, there were numerous small‐effect QTLs at southern sites, indicating a genotype‐by‐environment interaction in rust resistance loci. Interestingly, Prr1 and Prr2 had a strong epistatic interaction, which also varied in the strength and direction of effect across space. Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Furthermore, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.}, number={6}, journal={New Phytologist}, author={VanWallendael, A. and Bonnette, J. and Juenger, T.E. and Fritschi, F.B. and Fay, P.A. and Mitchell, R.B. and Lloyd-Reilley, J. and Rouquette, F.M. and Bergstrom, G.C. and Lowry, D.B.}, year={2020}, pages={1696–1708} }
 @article{vanwallendael_alvarez_franks_2020, title={Patterns of population genomic diversity in the invasive Japanese knotweed species complex}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85098895109&partnerID=MN8TOARS}, DOI={10.1101/2020.08.06.226886}, abstractNote={Abstract Premise Invasive species are expected to experience a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed ( Reynoutria japonica ), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity. Methods We used Genotyping-by-Sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used non-alignment based k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids. Results Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, Giant knotweed, and hybrid Bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, Giant knotweed and hybrids showed distinct population groups. We did not find evidence of Isolation-by-Distance in the species complex, likely reflecting the stochastic introduction history of this species complex. Among species, we found no correlations between SNPs and several temperature- and precipitation-based climatic variables. Conclusions The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.}, journal={bioRxiv}, author={VanWallendael, A. and Alvarez, M. and Franks, S.J.}, year={2020} }
 @book{vanwallendael_soltani_emery_peixoto_olsen_lowry_2019, title={A Molecular View of Plant Local Adaptation: Incorporating Stress-Response Networks}, volume={70}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85065097399&partnerID=MN8TOARS}, DOI={10.1146/annurev-arplant-050718-100114}, abstractNote={Ecological specialization in plants occurs primarily through local adaptation to different environments. Local adaptation is widely thought to result in costly fitness trade-offs that result in maladaptation to alternative environments. However, recent studies suggest that such trade-offs are not universal. Further, there is currently a limited understanding of the molecular mechanisms responsible for fitness trade-offs associated with adaptation. Here, we review the literature on stress responses in plants to identify potential mechanisms underlying local adaptation and ecological specialization. We focus on drought, high and low temperature, flooding, herbivore, and pathogen stresses. We then synthesize our findings with recent advances in the local adaptation and plant molecular biology literature. In the process, we identify mechanisms that could cause fitness trade-offs and outline scenarios where trade-offs are not a necessary consequence of adaptation. Future studies should aim to explicitly integrate molecular mechanisms into studies of local adaptation.}, journal={Annual Review of Plant Biology}, author={Vanwallendael, A. and Soltani, A. and Emery, N.C. and Peixoto, M.M. and Olsen, J. and Lowry, D.B.}, year={2019}, pages={559–583} }
 @article{vanwallendael_2019, title={Digest: Species collapse from disturbance occurs quickly, and recovery is slow*}, volume={73}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85070951198&partnerID=MN8TOARS}, DOI={10.1111/evo.13794}, abstractNote={In certain conditions, newly‐formed species pairs may revert to one species. Zhang et al. modeled the impact of disturbance on incipient species in a predator‐prey model and found that species collapse may occur rapidly following disturbance. A distinct species pair can sometimes be re‐established if previous conditions are restored, but this depends on the type of disturbance as well as the amount of time that passes after a collapse.}, number={8}, journal={Evolution}, author={VanWallendael, A.}, year={2019}, pages={1679–1680} }
 @article{vanwallendael_bonnette_juenger_fritschi_fay_mitchell_lloyd-reilley_rouquette_bergstrom_lowry_2019, title={Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85095634702&partnerID=MN8TOARS}, DOI={10.1101/619148}, abstractNote={Summary Local adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described. To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust ( Puccinia spp. ) severity in switchgrass ( Panicum virgatum ) plantings at eight locations across the central United States for three years and conducted quantitative trait locus (QTL) mapping for rust progression. We mapped several variable QTLs, but two large-effect QTLs which we have named Prr1 and Prr2 were consistently associated with rust severity in multiple sites and years, particularly in northern sites. In contrast, there were numerous small-effect QTLs at southern sites, indicating a genotype-by-environment interaction in rust resistance loci. Interestingly, Prr1 and Prr2 had a strong epistatic interaction, which also varied in strength and direction of effect across space. Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Further, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.}, journal={bioRxiv}, author={VanWallendael, A. and Bonnette, J. and Juenger, T.E. and Fritschi, F.B. and Fay, P.A. and Mitchell, R.B. and Lloyd-Reilley, J. and Rouquette, F.M. and Bergstrom, G.C. and Lowry, D.B.}, year={2019} }
 @article{vanwallendael_hamann_franks_2018, title={Evidence for plasticity, but not local adaptation, in invasive Japanese knotweed (Reynoutria japonica) in North America}, volume={32}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85047431482&partnerID=MN8TOARS}, DOI={10.1007/s10682-018-9942-7}, number={4}, journal={Evolutionary Ecology}, author={VanWallendael, A. and Hamann, E. and Franks, S.J.}, year={2018}, pages={395–410} }
 @article{kottler_vanwallendael_franks_2018, title={Experimental treatment with a hypomethylating agent alters lifehistory traits and fitness in brassica rapa}, volume={2018}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85062794663&partnerID=MN8TOARS}, DOI={10.1155/2018/7836845}, abstractNote={Epigenetic modifications to DNA can be inherited and may play a key role in evolution, with epigenetic influences on life history traits such as the timing of germination and flowering thought to be particularly important in plants. However, few studies have examined the effects of epigenetic modifications through experimental alteration of the methylome under differential growth conditions. In this study, we chemically induced global DNA hypomethylation using 5-azacytidine in three Brassica rapa plant populations differing in life history characteristics and under differing photoperiod treatments. We found that our 5-azacytidine treatment affected the timing of germination and that this effect differed across populations, with the treatment delaying germination in B. rapa Fast Plants, which have been artificially selected for rapid cycling, but accelerating germination in biennials. Rapid cycling B. rapa plants also were smaller and had lower reproductive fitness under the experimental demethylation treatment. There was no main effect of demethylation or photoperiod on flowering time, but the interaction was marginally significant, indicating that demethylation effects on flowering time depend on photoperiod. These results demonstrate that epigenetic modifications can influence phenotypic traits in ways that are dependent on genetic identity, life history, and light availability.}, journal={Journal of Aging Research}, author={Kottler, E.J. and VanWallendael, A. and Franks, S.J.}, year={2018} }