Charles H. Cannon

Communities contain closely related species during ecosystem disturbance

Predicting community and species responses to disturbance is complicated by incomplete knowledge about species traits. A phylogenetic framework should partially solve this problem, as trait similarity is generally correlated with species relatedness, closely related species should have similar sensitivities to disturbance. Disturbance should thus result in community assemblages of closely related species. We tested this hypothesis with 18 disturbed and 16 reference whole-lake, long-term zooplankton data sets. Regardless of disturbance type, communities generally contained more closely related species when disturbed. This effect was independent of species richness, evenness, and abundance. Communities already under stress (i.e., those in acidic lakes) changed most when disturbed. Species sensitivities to specific disturbances were phylogenetically conserved, were independent of body size, and could be predicted by the sensitivities of close relatives within the same community. Phylogenetic relatedness can effectively act as a proxy for missing trait information when predicting community and species responses to disturbance.

Exploiting sparseness in de novo genome assembly

BackgroundThe very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments.MethodsIn this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k- mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer.ResultsWe implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k- mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.

Rubber and pulp plantations represent a double threat to Hainan's natural tropical forests

Hainan, the largest tropical island in China, belongs to the Indo-Burma biodiversity hotspot and harbors large areas of tropical forests, particularly in the uplands. The Changhua watershed is the cradle of Hainans main river and a center of endemism for plants and birds. The watershed contains great habitat diversity and is an important conservation area. We analyzed the impact of rubber and pulp plantations on the distribution and area of tropical forest in the watershed, using remote sensing analysis of Landsat images from 1988, 1995 and 2005. From 1988 to 1995, natural forest increased in area (979-1040xa0sqxa0km) but decreased rapidly (763xa0sqxa0km) over the next decade. Rubber plantations increased steadily through the study period while pulp plantations appeared after 1995 but occupied 152xa0sqxa0km by 2005. Rubber and pulp plantations displace different types of natural forest and do not replace one another. Because pulp is not as profitable as rubber and existing pulp processing capacity greatly exceeds local supply, considerable pressure exists on remaining upland forests. We recommend for future management that these plantation forests be reclassified as industrial, making a clear policy distinction between natural and industrial forestry. Additionally, the local government should work to enforce existing laws preventing forest conversion on marginal and protected areas.

Tropical botanical gardens: at the in situ ecosystem management frontier.

Tropical botanical gardens (TBGs) should have a leading role in in situ conservation by directly promoting several initiatives, including the reintroduction of important or valuable native species, focused habitat restoration, assisted migration of species that are vulnerable to climate change, and creative local collaboration with governments, NGOs and indigenous peoples. Compared with temperate gardens, TBGs face heightened challenges for ex situ conservation, including greater absolute amounts of biodiversity, need for resource mobilization, risk of introducing invasive species and potential genetic introgression within living collections. Meanwhile, the ecosystems surrounding TBGs have undergone widespread and rapid conversion. Here, we provide several illustrations of the effectiveness of TBGs in achieving their mission of preserving tropical biodiversity at the frontier of in situ ecosystem management.

Pollinator sharing and gene flow among closely related sympatric dioecious fig taxa.

Hybridization and insect pollination are widely believed to increase rates of plant diversification. The extreme diversity of figs (Ficus) and their obligate pollinators, fig wasps (Agaonidae), provides an opportunity to examine the possible role of pollinator-mediated hybridization in plant diversification. Increasing evidence suggests that pollinator sharing and hybridization occurs among fig taxa, despite relatively strict coevolution with the pollinating wasp. Using five sympatric dioecious fig taxa and their pollinators, we examine the degree of pollinator sharing and inter-taxa gene flow. We experimentally test pollinator preference for floral volatiles, the main host recognition signal, from different figs. All five fig taxa shared pollinators with other taxa, and gene flow occurred between fig taxa within and between sections. Floral volatiles of each taxon attracted more than one pollinator species. Floral volatiles were more similar between closely related figs, which experienced higher levels of pollinator sharing and inter-taxa gene flow. This study demonstrates that pollinator sharing and inter-taxa gene flow occurs among closely related sympatric dioecious fig taxa and that pollinators choose the floral volatiles of multiple fig taxa. The implications of pollinator sharing and inter-taxa gene flow on diversification, occurring even in this highly specialized obligate pollination system, require further study.

A Curiosity Moment for Tropical Biology

I was truly amazed by the remarkable feat that NASAs Jet Propulsion Laboratory pulled off in landing the Curiosity rover on the surface of Mars. But it leaves me wondering whether we have ever spent a billion dollars examining any part of Earths tropical rainforest.nn![Figure][1] nnCREDIT: CHRISTIAN ZIEGLER/WIKIMEDIA COMMONSnnWe remain ignorant of even the most basic properties of Earths equatorial forests, such as the number of large mammal species (or invertebrates, fungi, and microbes) in a forest, and their life cycles. The information that we do have is biased toward small intensively studied areas, whereas the vast intervening areas remain largely unexamined. The most extensive global network of observation plots, managed by the Center for Tropical Forest Science, encompasses a tiny fraction of total forest area. Acquiring a comprehensive knowledge of these forests seems impossible. Yet so did walking on the Moon 50 brief years ago.nnThere are tremendous technical challenges in navigating the canopy of the tropical rainforests. We need to view the study of rainforests as an engineering problem and develop the same kind of amazing technologies used to study the surface of Mars. I want to be able to hover in a little car above the trees. I want to release a small cat-like autonomous robot into the canopy and retrieve it a month later two kilometers away, all the while tracking its movements as it gathers samples and observations, downloading gigabytes of data each day. There would be tremendous opportunities to translate those technologies into useful applications on Earth. I am confident that the trickle down would be much more substantial than that from the space program.nnAre we really going to have a colony on the Moon? Do we really plan on escaping to the stars? We have a few challenges here on Earth that we need to face before we can ever truly fulfill those dreams.nn [1]: pending:yes

Lithocarpus pulongtauensis (Fagaceae), a New Species from Borneo

We describe a new species of Lithocarpus from the central Kelabit Highlands of Sarawak, Malaysia with a distribution extending north to Mt. Kinabalu, Sabah. This species was included in a previous morphometric and phylogenetic study of the section Synaedrys, mistakenly identified as L. rotundatus. Several individuals were observed on the western slopes of Mt. Kinabalu between the elevation of 1200–1500 meters. The species has a distinctive cupule, which usually completely encloses the nut and is very dark in color, almost black with a brittle texture similar to charcoal. The fruit is semi-hemispheric in shape and the bracts on the cupule are entirely fused, relatively sparse, stiff, brittle, and prominent.