Norman A. Bourg

Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities

The study of biodiversity has tended to focus primarily on relatively information-poor measures of species diversity. Recently, many studies of local diversity (alpha diversity) have begun to use measures of functional and phylogenetic alpha diversity. Investigations into the phylogenetic and functional dissimilarity (beta diversity) of communities have been far less numerous, but these dissimilarity measures have the potential to infer the mechanisms underlying community assembly and dynamics. Here, we relate levels of phylogenetic and functional alpha diversity to levels of phylogenetic and functional beta diversity to infer the mechanism or mechanisms responsible for the assembly of tree communities in six forests located in tropical and temperate latitudes. The results show that abiotic filtering plays a role in structuring local assemblages and governing spatial turnover in community composition and that phylogenetic measures of alpha and beta diversity are not strong predictors of functional alpha and beta diversity in the forests studied.

Scale‐dependent relationships between tree species richness and ecosystem function in forests

1. The relationship between species richness and ecosystem function, as measured by productivity or biomass, is of long-standing theoretical and practical interest in ecology. This is especially true for forests, which represent a majority of global biomass, productivity and biodiversity.

First steps toward an electronic field guide for plants

We describe an ongoing project to digitize information about plant specimens and make it available to botanists in the field. This first requires digital images and models, and then effective retrieval and mobile computing mechanisms for accessing this information. We have almost completed a digital archive of the collection of type specimens at the Smithsonian Institution Department of Botany. Using these and additional images, we have also constructed prototype electronic field guides for the flora of Plummers Island. Our guides use a novel computer vision algorithm to compute leaf similarity. This algorithm is integrated into image browsers that assist a user in navigating a large collection of images to identify the species of a new specimen. For example, our systems allow a user to photograph a leaf and use this image to retrieve a set of leaves with similar shapes. We measured the effectiveness of one of these systems with recognition experiments on a large dataset of images, and with user studies of the complete retrieval system. In addition, we describe future directions for acquiring models of more complex, 3D specimens, and for using new methods in wearable computing to interact with data in the 3D environment in which it is acquired.

Plant diversity increases with the strength of negative density dependence at the global scale

Maintaining tree diversity Negative interaction among plant species is known as conspecific negative density dependence (CNDD). This ecological pattern is thought to maintain higher species diversity in the tropics. LaManna et al. tested this hypothesis by comparing how tree species diversity changes with the intensity of local biotic interactions in tropical and temperate latitudes (see the Perspective by Comita). Stronger local specialized biotic interactions seem to prevent erosion of biodiversity in tropical forests, not only by limiting populations of common species, but also by strongly stabilizing populations of rare species, which tend to show higher CNDD in the tropics. Science, this issue p. 1389; see also p. 1328 A global analysis of ~3000 species and ~2.4 million trees elucidates variations in tree species diversity between tropical and temperate latitudes. Theory predicts that higher biodiversity in the tropics is maintained by specialized interactions among plants and their natural enemies that result in conspecific negative density dependence (CNDD). By using more than 3000 species and nearly 2.4 million trees across 24 forest plots worldwide, we show that global patterns in tree species diversity reflect not only stronger CNDD at tropical versus temperate latitudes but also a latitudinal shift in the relationship between CNDD and species abundance. CNDD was stronger for rare species at tropical versus temperate latitudes, potentially causing the persistence of greater numbers of rare species in the tropics. Our study reveals fundamental differences in the nature of local-scale biotic interactions that contribute to the maintenance of species diversity across temperate and tropical communities.

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology.

Conspecific negative density-dependent mortality and the structure of temperate forests

Factors that control tree seedling dynamics are critical determinants of forest diversity. We examined the role of density-dependent mortality and abiotic factors in the differential establishment and survival of tree seedlings at three, large, mapped forest plots in Indiana, Virginia, and Wisconsin, USA. We tested whether seedling densities and seedling survival are related to local biotic and abiotic factors with generalized linear mixed models. Spatial point pattern analyses were utilized to determine if the distribution patterns of seedlings and saplings are consistent with a pattern generated by negative density-dependent mortality with respect to conspecific trees. Initial sampled seedling density for nearly a third of species showed a positive correlation with increasing conspecific basal area, indicating dispersal limitation, but few had any association with abiotic variables. By contrast, survival of seedlings over one year significantly declined with increasing conspecific basal area. Point pattern analyses indicated that nearly one-third of tree species had significantly over-dispersed point patterns of conspecific seedlings and saplings relative to adult densities; the majority of other species exhibited random spatial arrangements. Our results demonstrate that negative conspecific density-dependent mortality of seedlings could generate the spatial patterns observed at later life stages. By differentially favoring seedlings of other species, this process may contribute to the maintenance of tree diversity in temperate forests, just as others have demonstrated for tropical forests.

Initial census, woody seedling, seed rain, and stand structure data for the SCBI SIGEO Large Forest Dynamics Plot

Abstract We present data from the first five years (2008–2012) of the establishment of the 25.6-ha Smithsonian Conservation Biology Institute (SCBI) Large Forest Dynamics Plot, comprising the initial woody stem census, woody seedling plot surveys, seed rain, and dendrochronological data. The plot is in mature secondary mixed deciduous forest 5 km south of Front Royal, Virginia, USA. The initial plot census enumerated 38 932 free-standing living stems and 29 991 living individuals ≥1 cm dbh comprising 62 species, 38 genera, and 26 families, along with an additional 1248 dead/missing standing stems, for a total of 40 180 stems. Dominant canopy trees include tulip poplar (Liriodendron tulipifera), hickories (Carya spp.), oaks (Quercus spp.), white ash (Fraxinus americana), and black gum (Nyssa sylvatica). Prominent understory components include spicebush (Lindera benzoin), pawpaw (Asimina triloba), American hornbeam (Carpinus caroliniana), witchhazel (Hamamelis virginiana), and eastern redbud (Cercis canaden...

Effects of Twenty Years of Deer Exclusion on Woody Vegetation at Three Life-History Stages in a Mid-Atlantic Temperate Deciduous Forest

Abstract Chronic browsing by Odocoileus virginianus (White-tailed Deer) has potential to alter the life history of trees within Mid-Atlantic forests, including seedling size and abundance in the short term to overstory composition in the long term. Most studies quantify the effects of deer browse using small plots (<1 ha) and short time frames (<10 years), which may misrepresent larger-scale and longer-term impacts. We maintained a 4-ha deer exclusion plot for 20 years in a mesic northern Virginia temperate deciduous forest to examine the impacts of browsing on forest trees at multiple life-history stages. We compared the abundance and species composition, as well as seedling height, of woody stems across the seedling, small-sapling, and large-sapling size classes inside the deer exclosure and within an adjacent reference area. There were no significant differences in seedling abundance or community composition, but seedling height was on average 2.25 times greater in the exclosure than the reference plot. Small-sapling (1–5 cm DBH) stem count was 4.1 times greater inside the exclosure, with all species more abundant in the exclosure except Asimina triloba (Pawpaw) and Carya tomentosa (Mockernut Hickory). Differences were smaller in the large-sapling size class (5–10 cm DBH), with relative total large-sapling stem count only 1.25 times greater in the exclosure. Browsing pressure appeared to influence the composition and size structure of smaller stems in the past 20 years, but has had little effect on larger stems. While the lack of replication limited the scope of inference of our study, our findings suggest that natural delays in mature tree recruitment in a closed-canopy forest may mask the full impact of deer herbivory for decades.

Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.

Long-Term Effects of White-Tailed Deer Exclusion on the Invasion of Exotic Plants: A Case Study in a Mid-Atlantic Temperate Forest.

Exotic plant invasions and chronic high levels of herbivory are two of the major biotic stressors impacting temperate forest ecosystems in eastern North America, and the two problems are often linked. We used a 4-ha deer exclosure maintained since 1991 to examine the influence of a generalist herbivore, white-tailed deer (Odocoileus virginianus), on the abundance of four exotic invasive (Rosa multiflora, Berberis thunbergii, Rubus phoenicolasius and Microstegium vimineum) and one native (Cynoglossum virginianum) plant species, within a 25.6-ha mature temperate forest dynamics plot in Virginia, USA. We identified significant predictors of the abundance of each focal species using generalized linear models incorporating 10 environmental and landscape variables. After controlling for those predictors, we applied our models to a 4-ha deer exclusion site and a 4-ha reference site, both embedded within the larger plot, to test the role of deer on the abundance of the focal species. Slope, edge effects and soil pH were the most frequent predictors of the abundance of the focal species on the larger plot. The abundance of C. virginianum, known to be deer-dispersed, was significantly lower in the exclosure. Similar patterns were detected for B. thunbergii, R. phoenicolasius and M. vimineum, whereas R. multiflora was more abundant within the exclosure. Our results indicate that chronic high deer density facilitates increased abundances of several exotic invasive plant species, with the notable exception of R. multiflora. We infer that the invasion of many exotic plant species that are browse-tolerant to white-tailed deer could be limited by reducing deer populations.