Species in the early stages of domestication, in which wild and cultivated forms co-occur, provide important opportunities to develop and test hypotheses about the origins of crop species. Chrysophyllum cainito (Sapotaceae), the star apple or caimito, is a semidomesticated tree widely cultivated for its edible fruits; it is known to be native to the neotropics, but its precise geographic origins have not been firmly established. Here, we report results of microsatellite marker analyses supporting the hypothesis that the center of domestication for caimito was the Isthmus of Panama, a region in which few crop species are believed to have originated, despite its importance as a crossroads for the dispersal of domesticated plants between North and South America. Our data suggest that caimito was domesticated in a geographically restricted area while incorporating a diverse gene pool. These results refute the generally accepted Antillean origin of caimito, as well as alternative hypotheses that the species was domesticated independently in the two areas or over a broad geographic range including both. Human-mediated dispersal from Panama to the north and east was accompanied by strong reductions in both genotypic and phenotypic diversity. Within Panama, cultivated and wild trees show little neutral genetic divergence, in contrast to striking phenotypic differentiation in fruit and seed traits. In addition to providing a rare example of data that support the hypothesis of a narrow geographic origin on the Isthmus of Panama for a now widespread cultivated plant species, this study is one of the first investigations of the origins of an edible species of the large pantropical family Sapotaceae 

Sustainable forestry has been practiced for over a hundred years on the 16,000 ha of commercial forest lands on Joint Base Lewis-McChord. In the latter half of the 20^thcentury, the invasive shrub Scotch broom spread across the base, creating new challenges for reforestation efforts. Large areas of forest were essentially taken over by Scotch broom after trees were harvested.  Plantations have shown repeated failures, resulting in serious financial losses as well as a negative effect on military training. The primary objective of our project was to examine the impact of Scotch broom on establishment and growth of Douglas fir seedlings, and the effectiveness of different approaches to Scotch broom control in the forestry context. Here we report results from a number of related studies on [1] Douglas fir survival in previously invaded clearcuts, [2] Edge effects on Douglas fir survival, [3] Stimulating germination with disturbance, [4] Increase in Scotch broom cover after initial removal, [5]Variation across seasons in the effectiveness of Garlon 4 (triclopyr) herbicide, and [6]Legacy effects: Scotch broom effects on soil.

1. Douglas fir survival in previously invaded clearcuts. We set up a large-scale experiment (6.3ha total treatment area) with 12 treatments at 5 sites. We planted 7,448 two-year-old Douglas fir seedlings in March 2008 and censused 3,800 focal trees. In response to very high mortality, we replanted all focal trees in November 2008 or in March 2009. By September 2009, over 90% of these tree seedlings had died. This was the first documented evidence that direct competition from Scotch broom was not involved in Douglas fir plantation failure. Rather, soil or other abiotic conditions in the invaded clearcuts made these sites inhospitable to Douglas fir regeneration. We found no significant difference in survival between trees planted in November and trees planted in March.

2. Edge effects on Douglas fir survival. In a smaller study of 424 tree seedlings planted at different distances from two forest edges, we found a significant effect of distance from the nearest adult tree, and no difference between a north-facing and a south-facing edge, on survival through the first year. In another related study in March 2009, we planted Douglas fir seedlings along the edges of the same clearcuts described above, and we found higher survival along those edges than in the center of the clearcuts.

3. Stimulating germination with disturbance. Soil scarification is thought to stimulate germination of Scotch broom seeds out of the seedbank, relative to germination from seeds below established vegetation.We tested whether this effect of scarification is due to the physical disturbance of the soil or simply due to the removal of shade and competing vegetation. We compared Scotch broom germination from (1) control plots that had two-year-old undisturbed vegetation including Scotch broom, (2) plots scarified the previous year, and (3) plots treated with triclopyr the previous year. We found that both treatments had significantly more germination relative to the control, showing that part of the response to scarification is simply the removal of competition from established vegetation. In addition, scarified plots had significantly higher germination than herbicide plots, confirming that soil disruption had an additional stimulating effect on Scotch broom germination.

4. Increase in Scotch broom cover after initial removal.We tracked the rate of increase in percent cover of the invader Scotch broom over time in five sites. Patterns of Scotch broom cover after two years closely tracked patterns of seedling density in the first year rather than patterns of stump resprouting. However, after three years, the rank order of Scotch broom cover began to diverge from the initial germination data.

5. Variation across seasons in the effectiveness of Garlon 4 (triclopyr) herbicide. Restoration experts differ in their opinions about when is the best time to treat Scotch broom, often advocating for the importance of targeting the peak flowering season, or the dry season when the plant is most stressed. We quantified the effectiveness of chemical control in different seasons, spraying whole plots (56’ x 56’) with Garlon 4 Ultra (triclopyr) in March, May, or September of 2009, and measuring percent cover of Scotch broom in 2010. For this short-term response, all the spray treatments had strong effects relative to controls, and the effect of treatment seasonality was very small by comparison.

6. Legacy effects: Scotch broom effects on soil. Scotch broom is a nitrogen-fixing plant and therefore may ‘fertilize’ soils with increased N. At the same time, however, the plant produces N-rich defense compounds (alkaloids) that have been shown elsewhere to inhibit the growth and activity of some plants and microbes. Both of these effects may affect Douglas fir growth not only directly, but also indirectly via mycorrhizal associations, which may themselves be altered by changes in soil chemistry. We did a 19-month greenhouse experiment comparing invaded and uninvaded soils, with amendments of Scotch broom “mulch” (plant material added) and activated carbon (to bind allelochemicals). Both Douglas fir growth and mycorrhizal colonization were suppressed in invaded soils. Adding Scotch broom mulch to uninvaded soils increased Douglas fir growth, suggesting a nitrogen fertilization effect, but only in the presence of activated carbon.

The pest plant Scotch broom (Cytisus scoparius) is hindering effective reforestation at Fort Lewis, resulting in both a loss of land available for military training as well as a loss of native forest habitat for native plants and animals. Our primary objective was to examine the relative effectiveness of different broom control strategies that are appropriate for the forestry context, where the use of fire is not permitted. This document reports on the first year’s activities of a large research collaboration between personnel at the University of California Santa Cruz and at Fort Lewis. Key research questions include: What are the costs and benefits of an extended preliminary treatment phase, including two or even three years of soil scarification and control of small broom plants before planting? What is the relative effectiveness of chemical and mechanical treatment?

We set up a large-scale experiment (6.3ha total treatment area) at 5 sites, with a blocked design of 4 blocks per site with 6 plots per block. The plots were 56’x56’, designed to accommodate 49 tree seedlings (7x7) at 8’ spacing.  Scotch broom plants were removed from the entire site in fall of 2007 before the start of the experiment. We quantified Scotch broom stump density, mean diameter and height in each plot, as well as stump resprout rate and number of seedlings in spring of 2008. Initial stump density and size varied across sites. The resprout rate was low in four of the five sites, averaging 4 - 13% of stumps, but one site showed a very high resprout rate of 36%. Average seedling density, representing germination from the seedbank, varied across sites from <5 seedlings/m²to >100 seedlings/m². Most of the variation in seedling number was among sites (56%), followed by small-scale variation from quadrat to quadrat (30%), and plot to plot (12%). Almost no variation was seen across blocks within sites. We planted 7,448 two-year-old Douglas fir seedlings in March 2008. Over half of all Douglas fir seedlings died between March and September in almost all blocks, with close to 100% of the trees dying in one site, and over 80% of trees dying in some of the blocks of all sites. This was an unexpectedly high mortality rate, substantially higher mortality in these invaded clearcuts than mortality seen in other reforestation projects in smaller forest clearings on Fort Lewis.

Invasive species can change the environment in ways that persist long after the species itself is gone, called a "legacy effect." Legacy effects of invasive species include changes to the abiotic and biotic soil environment and can lead to positive feedbacks that inhibit restoration success and reinforce invasion. The objective of this research was to examine the legacy of Cytisus scoparius italic>your words, an aggressive nitrogen-fixing shrub, on soil chemistry, ectomycorrhizal fungi, and Douglas-fir forest regeneration. My work highlights the importance of allelopathy and nitrogen enrichment in the disruption of the mutualism between Douglas-fir and ectomycorrhizal fungi.

The temporal aspects of biological invasions are important and understudied. The impacts of invasive species may change in magnitude and even direction with time following invasion. In a novel contribution, I used a combination of field and greenhouse experiments to determine how soil legacies develop, persist and change over time.

I found that soils invaded by C. scoparius italic>your words harbor less ectomycorrhizal fungi, and that growth of Douglas-fir is linked to the abundance of these fungi. Adding C. scoparius italic>your words mulch into uninvaded forest soils revealed that Douglas-fir grew more when mulch was added, but only in the presence of activated carbon, suggesting that allelopathy may be inhibiting Douglas-fir success.

To examine how long soil legacies persist after C. scoparius removal, I removed C. scoparius italic>your words at different times over a 22-month period, then measured soil properties. One month following C. scoparius italic>your words removal, nitrogen availability increased, but by 10 months, dropped to less than what was found in live C. scoparius stands italic>your words, suggesting that the legacy of nitrogen enrichment is not stable and declines with time following removal. Following C. scoparius italic>your words removal, exotic grasses quickly established and dominated the sites, and they may contribute to the suppression of Douglas-fir seedling growth. I also used a chronosequence approach to assess how quickly soil-mediated impacts develop after invasion. I planted Douglas-fir into soils collected from C. scoparius italic>your words invasions of different ages. Suprisingly, the seedlings grew larger in soils that had been invaded longer; in this case nitrogen fertilization seems to be more important than other effects of C. scoparius italic>your words invasion.

At Joint Base Lewis-McChord, tree plantations have failed repeatedly in areas that had once supported Douglas fir forest, with Scotch broom invasion replacing forest. Maximizing the effectiveness of Scotch broom control is a top management priority. The studies presented here have two main foci: timing of control relative to the Scotch broom life cycle, and chemical vs. manual control. We also explore the effects of forest edges on Douglas fir seedling survival and mycorrhizal colonization. 

We set up a large-scale experiment (6.3ha total treatment area) at 5 heavily invaded sites in which all broom was mechanically removed in 2007. Each site contained 4 blocks of 12 treatments. We measured density of newly germinated seedlings using 24m-long, 10cm-wide belt transects, and percent cover of Scotch broom using line-intercept method on 24m transects.

Seedling density (representing germination from the seedbank) peaked in year 2 and varied dramatically among sites, with one site showing an averageof nearly 350 seedlings/m².

Scotch broom percent cover in control plots increased most rapidly between years 2 and 3, by the fourth year reaching over 150% cover in one site and around 100% cover in two other sites. In contrast, the slowest growing site had only about 20% cover after four years. Plant size also varied across sites. By the fourth year, average plant height was around 2.5m in two of the sites, but only around 1m in the slowest growing site.

Chemical vs. mechanical control of seedlings.

We compared different approaches to removing broom seedlings at a large scale. Mechanical control comprised “scarifying” the soil to scrape off all seedlings with a mulcher, while chemical control was a broadcast spray of triclopyr herbicide.  We also compared a single scarify treatment to multiple years of treatment (to stimulate and then exhaust the seedbank). With percent cover three years later as the response variable, we found few generalizable differences among treatments. In two sites, herbicide strongly reduced (by over 75%) Scotch broom cover. In one site, multiple years of scarification reduced (by about 50%) cover.

Chemical control across seasons.

We incorporated the question of seasonality into the herbicide component of our experiment because of a lack of consensus among practitioners about the best time of year to spray Scotch broom. We sprayed whole plots (56’ x 56’) with Garlon 4 Ultra (triclopyr) in March, May, or September of 2009, and quantified percent cover of Scotch broom in 2012. All the spray treatments had strongly reduced broom cover relative to controls, with the exception of one site that had very low cover altogether. The effect of the treatment did not vary with season in four of the five sites. In the fifth site, March spray was less effective.

Chemical vs. mechanical control of older plants.

We compared brushcutting to triclopyr spray on 2.5-year old plants in September 2010,.  Herbicide led to a significantly higher kill rate per plant, consistently 80-95% across all sites, compared to variable rates (25-95%) for brush cutting. However, two years later percent cover of Scotch broom was showing only a non-significant trend toward better results with herbicide. Both brushcutting and triclopyr spray strongly reduced percent cover of Scotch broom compared to the untreated control in all but one site. 

Edge effects, soil inoculum, and mycorrhizae.

Our early studies suggested that Douglas-fir seedlings planted near adult trees or forest edges established with much higher success than more isolated seedlings. We did a large-scale, well-replicated experiment to test whether tree establishment was consistently higher near forest edges, and also whether mycorrhizal fungi play a role in this edge effect. At the same five sites, we established transects along forest edges and paired transects 15-25m out into the clearcut. We planted 958 Douglas fir seedlings, and we transplanted soil with each seedling: half received forest soil and the other half received soil from the invaded clearcut. Survival was much higher on the forest edge, and mycorrhizal colonization was also higher on the edge.  However, the effect of transplanting soil inoculum was not significant, and even the non-significant trend disappeared completely by the second year. Our results suggest that sites that are otherwise inhospitable for young trees and in which plantations have failed may still show potential to regenerate slowly, starting at the edges. These results also have implications for how the geometry of forest harvest methods influences reforestation success.

This work examines plant response to human alteration in deserts and coastal salt marshes, two systems in which abiotic stress is assumed to limit plants more strongly than biotic factors.

In the desert, I used experimental panels to simulate the effect of solar energy infrastructure on two habitat types. I measured plant diversity and abundance, finding that panels interacted with rainfall and physical features of each habitat type to drive different outcomes. Under panels, diversity and abundance tended to be higher in one habitat type, but lower in the other. I also examined panel effects on the demography of a closely related rare-common species pair. Panel effects on individual demographic rates were rarely strong, but matrix models integrating these effects across the life cycle revealed a negative impact on the rare species, mediated by increased competition under panels. This result highlights the risk of using a common relative to predict impacts on a rare species.

In the coastal salt marsh, I tested whether the Stress Gradient Hypothesis (SGH) can be applied to improve restoration outcomes. The SGH framework predicts that interactions between plants should shift from competition to facilitation as stress increases. I found that soil conditions were more stressful (more negative water potential) at higher marsh elevations, so I expected clustered plantings to do better upslope. I planted two natives in loose and clustered patterns and tracked their performance across elevation for two years. Surprisingly, performance did not vary with elevation during the first year, while clustering had a negative effect on growth. After two years both species showed clear but inverse patterns of cover across elevation – yet across the entire elevation gradient, clustering strongly inhibited cover in both species.

My work demonstrates that even in “stressful” systems, abiotic stress is not always the dominant constraint on plants. To develop effective conservation and restoration strategies in these systems will require a deep understanding of how human disturbance interacts with the biotic and abiotic drivers that govern plant performance.

Ehrharta erecta (panic veldt grass) is an actively spreading invasive grass in California with an uncommon capacity to invade forest understory. Greater understanding of the ecology, impacts, and potential for control of this invader is needed to set priorities and guide management. In a mixed-evergreen forest in Santa Cruz County, we measured impacts of E. erecta on native plant species richness and abundance, quantified the effectiveness of mechanical and chemical management methods, and tested whether this species forms a seed bank. We found lower percent cover of native species in plots invaded by E. erecta compared to nearby non-invaded plots, but we did not find significant differences in species richness, and we did not find a significant relationship between E. erecta cover and native cover in invaded plots. Strikingly, we measured nearly four times greater total vegetation cover in E. erecta invaded plots. Twenty-two months following management treatments, we found significant reductions in E. erecta using both mechanical and chemical methods. Herbicide application produced greater non-target effects. In a separate experiment, we tested the effects of native plant addition on restoration outcomes and regrowth of E. erecta. Transplanting native Clinopodium douglasii into management plots did not slow regrowth of E. erecta. Transplants did increase the percent cover native plants, but only by increasing C. douglasii itself. Finally, in a greenhouse experiment we compared the number of E. erecta germinants from duff and soil collected from two depths. Ehrharta erecta germinated from all three substrates, with the greatest number of germinants in the upper soil layer, suggesting that E. erecta seeds accumulate in the soil over time. The results of this research demonstrate that E. erecta drives ecological change in a mixed-evergreen forest community, effective management is possible using manual and chemical removal methods, and restoration of native species can be promoted through planting. Since we found evidence that E. erecta forms a seed bank, we recommend rapid response to E. erecta invasion and consideration of management methods that have low soil disturbance in treating established E. erecta populations.

The rare species advantage postulates that dominant plant species experience greater disease pressure, as their abundance can support the spread of specialized pathogens. Yet most pathogens are not host specific – pathogen host ranges frequently encompass multiple closely related plant species, resulting in increased sharing of pathogens between closely phylogenetically related community members. We examined the role host phylogenetic rarity plays in pathogen spread in a diverse plant community by inserting novel hosts (non-native plant species newly introduced into a novel habitat) into a coastal grassland and identifying the patterns of pathogen spillover from resident plant species onto the novel hosts. We identified fungi present in leaf tissues of novel hosts via metagenomic sequencing of the fungal internal transcribed spacer (ITS) region to generate operational taxonomic units (OTUs). We found that 161/342 (47.1%) OTUs identified were singletons. Excluding singletons, the median number of novel plant species colonized by a given OTU was 4, and the mean was 11.5, while 19/181 (10.5%) of non-singleton OTUs were found on 14 (50%) or more novel hosts. The proportion of broad generalist and rare fungal taxa on novel hosts were similar to several other systems, including other grasslands, temperate and boreal forests, tropical rainforests, wetlands, and deserts. We did not find a relationship between phylogenetic relatedness of a novel host to the surrounding vegetation and the fungal species richness on that host. Weighting phylogenetic distance by local plant species abundance did not strengthen the relationship between phylogenetic distance and fungal richness on novel hosts.