Katrina M Dlugosch

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Scholarly Contributions

Books

• Barrett, S. C., Colautti, R. I., Dlugosch, K. M., & Rieseberg, L. H. (2016). Invasion genetics: The Baker and Stebbins legacy. Wiley.

Chapters

• Dlugosch, K. M., & Parker, I. M. (2016). Introduction: Evolutionary ecology. In Invasion genetics: The Baker and Stebbins Legacy. Wiley.
• Dlugosch, K. M., & Bonin, A. (2012). Allele identification in assembled genomic sequence datasets. In Data production and analysis in population genomics(pp 197-211). New York: Springer.

Journals/Publications

• Dlugosch, K. M., Enquist, B. J., Maitner, B. S., & Park, D. S. (2021).

  Where we've been and where we're going: the importance of source communities in predicting establishment success from phylogenetic relationships

  . Ecography. doi:10.1111/ecog.05406
• Barker, B. S., Andonian, K., Swope, S. M., Luster, D., & Dlugosch, K. M. (2015). Population genomic analyses reveal a history of range expansion and trait evolution in the invasive plant yellow starthistle (Centaurea solstitialis). Molecular Ecology.
• Dlugosch, K. M., Anderson, S. R., Braasch, J., Cang, F. A., & Gillette, H. D. (2015). The devil is in the details: genetic variation in introduced populations and its contributions to invasion. Molecular Ecology, 24, 2095-2111.
• Dlugosch, K. M., Cang, F. A., Barker, B. S., Andonian, K., Swope, S. M., & Rieseberg, L. H. (2015). Evolution of invasiveness through increased resource use in a vacant niche. Nature Plants, 1, 15066.
• Dlugosch, K. M., Lai, Z., Bonin, A., Hierro, J., & Rieseberg, L. H. (2013). Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis. G3: Genes, Genomes, Genetics, 3(2), 359-367.
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  Abstract: Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 112430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios. © 2013 Dlugosch et al.
• Lai, Z., Kane, N. C., Kozik, A., Hodgins, K. A., Dlugosch, K. M., Barker, M. S., Matvienko, M., Yu, Q., Turner, K. G., Pearl, S. A., Bell, G. D., Zou, Y., Grassa, C., Guggisberg, A., Adams, K. L., Anderson, J. V., Horvath, D. P., Kesseli, R. V., Burke, J. M., , Michelmore, R. W., et al. (2012). Genomics of compositae weeds: EST libraries, microarrays, and evidence of introgression. American Journal of Botany, 99(2), 209-218.
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  Premise of study: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we describe the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization.
• Li, Y. M., Dlugosch, K. M., & Enquist, B. J. (2015). Novel spatial analysis methods reveal scale‐dependent spread and infer limiting factors of invasion by Sahara mustard. Ecography, 38(3), 311–320.
• Mayrose, M., Kane, N. C., Mayrose, I., Dlugosch, K. M., & Rieseberg, L. H. (2011). Increased growth in sunflower correlates with reduced defences and altered gene expression in response to biotic and abiotic stress. Molecular Ecology, 20(22), 4683-4694.
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  PMID: 21988641;Abstract: Cultivated plants have been selected by humans for increased yield in a relatively benign environment, where nutrient and water resources are often supplemented, and biotic enemy loads are kept artificially low. Agricultural weeds have adapted to this same benign environment as crops and often have high growth and reproductive rates, even though they have not been specifically selected for yield. Considering the competing demands for resources in any plant, a key question is whether adaptation to agricultural environments has been accompanied by life history trade-offs, in which resistance to (largely absent) stress has been lost in favour of growth and reproduction. The experiments reported here were designed to test for growth-defence trade-offs in agricultural weeds, crops and native varieties of common sunflower (Helianthus annuus L., Asteraceae) by comparing their performance in the presence or absence of abiotic (drought and crowding) or biotic (simulated herbivory, insect herbivory and fungal) stress. We found that growth, as well as viability of crops and weeds, was reduced by abiotic drought stress. The weakened defence in the agricultural genotypes was further evident as increased susceptibility to fungal infection and higher level of insect palatability. To uncover molecular mechanisms underlying these trade-offs, we monitored gene expression kinetics in drought-stressed plants. By correlating phenotypic observations with molecular analyses, we report the identification of several genes, including a protein phosphatase 2C and the HD-Zip transcription factor Athb-8, whose expression is associated with the observed phenotypic variation in common sunflower. © 2011 Blackwell Publishing Ltd.
• Barker, M. S., Dlugosch, K. M., Dinh, L., Challa, R. S., Kane, N. C., King, M. G., & Rieseberg, L. H. (2010). EvoPipes.net: Bioinformatic tools for ecological and evolutionary genomics. Evolutionary Bioinformatics, 6, 143-149.
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  Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among the chief problems posed by next-generation sequencing are assembly and analyses of these large data sets. Here we present an online server, http://EvoPipes.net, that provides access to a wide range of tools for bioinformatic analyses of genomic data oriented for ecological and evolutionary biologists. The EvoPipes. net server includes a basic tool kit for analyses of genomic data including a next-generation sequence cleaning pipeline (SnoWhite), scaffolded assembly software (SCARF), a reciprocal best-blast hit ortholog pipeline (RBH Orthologs), a pipeline for reference protein-based translation and identification of reading frame in transcriptome and genomic DNA (TransPipe), a pipeline to identify gene families and summarize the history of gene duplications (DupPipe), and a tool for developing SSRs or microsatellites from a transcriptome or genomic coding sequence collection (findSSR). EvoPipes. net also provides links to other software developed for evolutionary and ecological genomics, including chromEvol and NU-IN, as well as a forum for discussions of issues relating to genomic analyses and interpretation of results. Overall, these applications provide a basic bioinformatic tool kit that will enable ecologists and evolutionary biologists with relatively little experience and computational resources to take advantage of the opportunities provided by next-generation sequencing in their systems.
• Dlugosch, K. M., Barker, M. S., & Rieseberg, L. H. (2010). NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform. BMC Research Notes, 3, 217.
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  There is increasing demand to test hypotheses that contrast the evolution of genes and gene families among genomes, using simulations that work across these levels of organization. The EvolSimulator program was developed recently to provide a highly flexible platform for forward simulations of amino acid evolution in multiple related lineages of haploid genomes, permitting copy number variation and lateral gene transfer. Synonymous nucleotide evolution is not currently supported, however, and would be highly advantageous for comparisons to full genome, transcriptome, and single nucleotide polymorphism (SNP) datasets. In addition, EvolSimulator creates new genomes for each simulation, and does not allow the input of user-specified sequences and gene family information, limiting the incorporation of further biological realism and/or user manipulations of the data.
• Barker, M. S., Dlugosch, K. M., Reddy, A. C., Amyotte, S. N., & Rieseberg, L. H. (2009). SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses. Bioinformatics, 25(4), 535-536.
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  Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together low-coverage 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences.
• Stewart Jr., C. N., Tranel, P. J., Horvath, D. P., Anderson, J. V., Rieseberg, L. H., Westwood, J. H., Mallory-Smith, C. A., Zapiola, M. L., & Dlugosch, K. M. (2009). Evolution of weediness and invasiveness: Charting the course for weed genomics. Weed Science, 57(5), 451-462.
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  Abstract: The genetic basis of weedy and invasive traits and their evolution remain poorly understood, but genomic approaches offer tremendous promise for elucidating these important features of weed biology. However, the genomic tools and resources available for weed research are currently meager compared with those available for many crops. Because genomic methodologies are becoming increasingly accessible and less expensive, the time is ripe for weed scientists to incorporate these methods into their research programs. One example is next-generation sequencing technology, which has the advantage of enhancing the sequencing output from the transcriptome of a weedy plant at a reduced cost. Successful implementation of these approaches will require collaborative efforts that focus resources on common goals and bring together expertise in weed science, molecular biology, plant physiology, and bioinformatics. We outline how these large-scale genomic programs can aid both our understanding of the biology of weedy and invasive plants and our success at managing these species in agriculture. The judicious selection of species for developing weed genomics programs is needed, and we offer up choices, but no Arabidopsis-like model species exists in the world of weeds. We outline the roadmap for creating a powerful synergy of weed science and genomics, given well-placed effort and resources. © Weed Science Society of America.
• Dlugosch, K. M., & Hays, C. G. (2008). Genotypes on the move: Some things old and some things new shape the genetics of colonization during species invasions. Molecular Ecology, 17(21), 4583-4585.
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  PMID: 18992002;Abstract: When we set a species loose outside of its historical range, we create opportunities to test fundamental questions about how populations establish, adapt, disperse, and ultimately define range boundaries. A particularly controversial issue here is how genetic variation among and within populations contributes to the dynamics of species distributions. In this issue of Molecular Ecology, Rosenthal and colleagues (2008) seize an opportunity to examine how multiple introductions create genetically distinct establishment events and how these are incorporated into invasive spread. Their findings suggest that a particular recombinant lineage of Brachypodium sylvaticum may be responsible for most of the recent expansion of this invader, highlighting the potential importance of genetic novelty and historical context for colonization success. © 2008 The Author.
• Dlugosch, K. M., & Parker, I. M. (2008). Founding events in species invasions: Genetic variation, adaptive evolution, and the role of multiple introductions. Molecular Ecology, 17(1), 431-449.
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  PMID: 17908213;Abstract: Invasive species are predicted to suffer from reductions in genetic diversity during founding events, reducing adaptive potential. Integrating evidence from two literature reviews and two case studies, we address the following questions: How much genetic diversity is lost in invasions? Do multiple introductions ameliorate this loss? Is there evidence for loss of diversity in quantitative traits? Do invaders that have experienced strong bottlenecks show adaptive evolution? How do multiple introductions influence adaptation on a landscape scale? We reviewed studies of 80 species of animals, plants, and fungi that quantified nuclear molecular diversity within introduced and source populations. Overall, there were significant losses of both allelic richness and heterozygosity in introduced populations, and large gains in diversity were rare. Evidence for multiple introductions was associated with increased diversity, and allelic variation appeared to increase over long timescales (∼100 years), suggesting a role for gene flow in augmenting diversity over the long-term. We then reviewed the literature on quantitative trait diversity and found that broad-sense variation rarely declines in introductions, but direct comparisons of additive variance were lacking. Our studies of Hypericum canariense invasions illustrate how populations with diminished diversity may still evolve rapidly. Given the prevalence of genetic bottlenecks in successful invading populations and the potential for adaptive evolution in quantitative traits, we suggest that the disadvantages associated with founding events may have been overstated. However, our work on the successful invader Verbascum thapsus illustrates how multiple introductions may take time to commingle, instead persisting as a 'mosaic of maladaptation' where traits are not distributed in a pattern consistent with adaptation. We conclude that management limiting gene flow among introduced populations may reduce adaptive potential but is unlikely to prevent expansion or the evolution of novel invasive behaviour. © 2007 The Authors.
• Dlugosch, K. M., & Parker, I. M. (2008). Invading populations of an ornamental shrub show rapid life history evolution despite genetic bottlenecks. Ecology Letters, 11(7), 701-709.
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  PMID: 18410377;Abstract: Human-mediated species introductions offer opportunities to investigate when and how non-native species to adapt to novel environments, and whether evolution has the potential to contribute to colonization success. Many long-established introductions harbour high genetic diversity, raising the possibility that multiple introductions of genetic material catalyze adaptation and/or the evolution of invasiveness. Studies of nascent invasions are rare but crucial for understanding whether genetic diversity facilitates population expansion. We explore variation and evolution in founder populations of the invasive shrub Hypericum canariense. We find that these introductions have experienced large reductions in genetic diversity, but that increased growth and a latitudinal cline in flowering phenology have nevertheless evolved. These life history changes are consistent with predictions for invasive plants. Our results highlight the potential for even genetically depauperate founding populations to adapt and evolve invasive patters of spread. © 2008 Blackwell Publishing Ltd/CNRS.
• Dlugosch, K. M., & Whitton, J. (2008). Can we stop transgenes from taking a walk on the wild side?. Molecular Ecology, 17(5), 1167-1169.
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  PMID: 18302682;Abstract: Whether the potential costs associated with broad-scale use of genetically modified organisms (GMOs) outweigh possible benefits is highly contentious, including within the scientific community. Even among those generally in favour of commercialization of GM crops, there is nonetheless broad recognition that transgene escape into the wild should be minimized. But is it possible to achieve containment of engineered genetic elements in the context of large scale agricultural production? In a previous study, Warwick et al. (2003) documented transgene escape via gene flow from herbicide resistant (HR) canola (Brassica napus) into neighbouring weedy B. rapa populations (Fig. 1) in two agricultural fields in Quebec, Canada. In a follow-up study in this issue of Molecular Ecology, Warwick et al. (2008) show that the transgene has persisted and spread within the weedy population in the absence of selection for herbicide resistance. Certainly a trait like herbicide resistance is expected to spread when selected through the use of the herbicide, despite potentially negative epistatic effects on fitness. However, Warwick et al.'s findings suggest that direct selection favouring the transgene is not required for its persistence. So is there any hope of preventing transgene escape into the wild? © 2008 The Authors.
• Whitton, J., Dlugosch, K. M., & Sears, C. J. (2008). Molecular and morphological evidence for and against gene flow in sympatric apomicts of the North American Crepis agamic complex (Asteraceae). American Journal of Botany, 86(8), 877-885.
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  Abstract: The study of sympatric populations of closely related plant species often reveals evidence of hybridization. Mechanisms that reduce outcrossing (e.g., selfing, apomixis) may allow co-occurrence without gene flow. In this study, we describe patterns of genetic variation in two contact zones, each comprising three closely related morphological types, that key to three distinct species in the North American Crepis agamic (apomictic) complex. We used RAPD markers to characterize individuals from two sites: one in northern California (Sardine Lookout) and another in northwestern Oregon (Summit Road). At Sardine Lookout, we discerned a total of four multilocus genotypes, two in one species, and one each in the other two species. Our findings suggest that distinct morphological types are maintained by absolute barriers to gene flow at this site. At Summit Road, we found greater genotypic diversity, with a total of 24 genotypes across 30 individuals. One of the morphological types was clearly genetically differentiated from the other two, with no variable markers shared with other species at this site. The two remaining species showed evidence of gene flow, with no unique markers discerning them. Morphological data tend to support this conclusion, with univariate and multivariate analyses indicating a pattern of variation spanning the two species. Taken together, these patterns suggest that contact zones need not represent hybrid zones, and that apomixis can serve as an effective barrier to gene flow that may allow for stable coexistence of close relatives. © 2008 NRC.
• Dlugosch, K. M., & Parker, I. M. (2007). Molecular and quantitative trait variation across the native range of the invasive species Hypericum canariense: Evidence for ancient patterns of colonization via pre-adaptation?. Molecular Ecology, 16(20), 4269-4283.
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  PMID: 17850270;Abstract: To understand the success of invasive species, it is important to know whether colonization events are facilitated by adaptive evolution or are limited to sites where a species is pre-adapted to thrive. Studies of the ancient colonization patterns of an invader in its native range provide an opportunity to examine its natural history of adaptation and colonization. This study uses molecular (internal transcribed spacer sequence and amplified fragment length polymorphism) and common garden approaches to assess the ancient patterns of establishment and quantitative trait evolution in the invasive shrub Hypericum canariense. This species has an unusually small and discrete native range in the Canary Islands. Our data reveal two genetic varieties with divergent life histories and different colonization patterns across the islands. Although molecular divergence within each variety is large (pairwise FST from 0.18 to 0.32 between islands) and nearly as great as divergence between them, life-history traits show striking uniformity within varieties. The discrepancy between molecular and life-history trait divergence points to the action of stabilizing selection within varieties and the influence of pre-adaptation on patterns of colonization. The colonization history of H. canariense reflects how the relationship between selective environments in founding and source populations can dictate establishment by particular lineages and their subsequent evolutionary stasis or change. © 2007 The Authors.
• Dlugosch, K. M. (2005). Understory community changes associated with english ivy invasions in Seattle's urban parks. Northwest Science, 79(1), 52-60.
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  Abstract: English ivy has become a common invader in Seattle's urban parks and in forests throughout the Pacific Northwest. Despite a great deal of concern over the potential impacts of this species, no studies have investigated ivy's effects on native vegetation in this region. In this study, paired comparisons between ivy-invaded and adjacent non-invaded plots in three Seattle parks were used to quantify changes associated with ivy invasion in the forest understory. Species diversity, percent cover, and tree regeneration were surveyed. Differences in species diversity, calculated as both richness and evenness, were not significantly different between invaded and non-invaded plots. Ivy-invaded plots did have significantly higher total cover, and significantly lower non-ivy cover, than non-invaded plots. The reduction of percent cover in invaded plots was primarily due to the loss of native shrubs. A plot where ivy had been removed over five years was also surveyed, and percent cover in this plot showed intermediate values relative to invaded and non-invaded plots, for both total cover and cover of native shrubs. The number of trees regenerating in the understory was higher in invaded plots, though this difference was not significant. These results suggest that English ivy invasions have substantial impacts on understory cover, and may influence the species composition and diversity of forest communities over the long-term by increasing vegetative cover and suppressing dominant native shrubs. © 2005 by the Northwest Scientific Association. All rights reserved.
• Dlugosch, K., & del Moral, R. (1999). Vegetational heterogeneity along elevational gradients. Northwest Science, 73(1), 12-18.
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  Abstract: How vegetation recovers from disturbance is a central ecological question. We tested the hypothesis that plant spatial heterogeneity declines with increasing functional vegetation age. As pioneers expand and more species invade, we expect heterogeneity to decline. Biomass accumulation and seedling recruitment both drive succession and proceed more slowly at higher elevation. Therefore, we predicted that higher elevation sites would be more heterogeneous than lower sites. We sampled vegetation in five habitats on Mount St. Helens to study recovery 17 years after its most recent eruption. Two lahars were undergoing primary succession and one ridge was recovering from nearly total destruction. A second ridge had been greatly impacted by the blast, while a fifth site was little damaged. Plant cover was analyzed using percentage similarity (PS) and detrended correspondence analysis (DCA). PS decreased with elevation on lahars and on the devastated ridge, but no clear trend was found on less impacted sites. The variation in DCA scores of samples at a site suggested increasing heterogeneity with elevation on one lahar and the strongly disturbed secondary site. The other transects did not show this pattern. These patterns support the hypothesis that heterogeneity declines with increasing successional age. Implicit in the hypothesis is that stochastic factors are important to the establishment of vegetation. High variability among samples of stable vegetation at lower elevation sites suggests that the effects of stochastic establishment can persist.
• Parker, I. M., Cuevas Garcia, E., Dlugosch, K. M., Holloran, P., Swope, S. M., Hulvey, K. B., & Clark, R. (1999). Invasions as a tool for basic research. Conservation Biology, 21(5), 1376-1377.
• Schultz, C. B., & Dlugosch, K. M. (1999). Nectar and hostplant scarcity limit populations of an endangered Oregon butterfly. Oecologia, 119(2), 231-238.
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  Abstract: As grassland habitats become degraded, declines in juvenile and adult food resources may limit populations of rare insects. Fender's blue butterfly (Icaricia icarioides fenderi), a species proposed for listing as endangered under the US Endangered Species Act, survives in remnants of upland prairie in western Oregon. We investigated the effects of limited larval hostplants and adult nectar sources on butterfly population size at four sites that encompass a range of resource densities. We used coarse and detailed estimates of resource abundance to test hypotheses relating resource quantity to population size. Coarse estimates of resources (percent cover of hostplant and density of nectar flowers) suggest that butterfly population size is not associated with resource availability. However, more detailed estimates of resources (density of hostplant leaves and quantity of nectar from native nectar sources) suggest that butterfly population size is strongly associated with resource availability. The results of this study suggest that restoring degraded habitat by augmenting adult and larval resources will play an important role in managing populations of this rare butterfly.