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|Strijk, J.S., Sirimongkol, S., Rueangruea, S., Ritphet, N. and Chamchumroon., V.
|Lithocarpus orbicarpus (Fagaceae), a new species of Stone Oak from Phang Nga province, Thailand.
Vol. 34, pp. 33–46
|Abstract:A new species is described, Lithocarpus orbicarpus Strijk, collected from Ton Pariwat Wildlife Sanctuary, Mueang district, Phang Nga Province in the Peninsular Floristic Region of Thailand. We provide the first technical illustrations and colour photographs of the new species, as well as a description of its conservation status and the collecting locality. The species can be easily distinguished by its unique orbicular acorns, each covered with a dense pattern of irregularly placed scales, which completely conceal the nut, except for a tiny apical pore, and which are arranged in a dense cluster on an erect woody spike. We also provide an amendment to the existing diagnostic key to Lithocarpus, and discuss important differences with morphologically similar species found in Thailand and the surrounding region.
@article{Strijk2014, author = {Strijk, J.S., Sirimongkol, S., Rueangruea, S., Ritphet, N. and Chamchumroon., V.}, title = {Lithocarpus orbicarpus (Fagaceae), a new species of Stone Oak from Phang Nga province, Thailand.}, journal = {PhytoKeys}, year = {2014}, volume = {34}, pages = {33–46}, url = {http://www.pensoft.net/journals/phytokeys/article/6429/abstract/lithocarpus-orbicarpus-fagaceae-a-new-species-of-stone-oak-from-phang-nga-province-thailand} }
|Van Welzen, P.C., Strijk, J.S., Van Konijnenburg-van Cittert, J.H.A., Nucete, M. and Merckx, V.S.F.T.
|Dated Phylogenies of the Sister Genera Macaranga and Mallotus (Euphorbiaceae): Congruence in Historical Biogeographic Patterns?
|PLoS ONE
Vol. 9(1): e85713. doi: 10.1371/journal.pone.0085713, pp. e85713
|Abstract:Molecular phylogenies and estimates of divergence times within the sister genera Macaranga and Mallotus were estimated using Bayesian relaxed clock analyses of two generic data sets, one per genus. Both data sets were based on different molecular markers and largely different samples. Per genus three calibration points were utilised. The basal calibration point (crown node of all taxa used) was taken from literature and used for both taxa. The other three calibrations were based on fossils of which two were used per genus. We compared patterns of dispersal and diversification in Macaranga and Mallotus using ancestral area reconstruction in RASP (S-DIVA option) and contrasted our results with biogeographical and geological records to assess accuracy of inferred age estimates. A check of the fossil calibration point showed that the Japanese fossil, used for dating the divergence of Mallotus, probably had to be attached to a lower node, the stem node of all pioneer species, but even then the divergence time was still younger than the estimated age of the fossil. The African (only used in the Macaranga data set) and New Zealand fossils (used for both genera) seemed reliably placed. Our results are in line with existing geological data and the presence of stepping stones that provided dispersal pathways from Borneo to New Guinea-Australia, from Borneo to mainland Asia and additionally at least once to Africa and Madagascar via land and back to India via Indian Ocean island chains. The two genera show congruence in dispersal patterns, which corroborate divergence time estimates, although the overall mode and tempo of dispersal and diversification differ significantly as shown by distribution patterns of extant species.
@article{Van2014, author = {Van Welzen, P.C., Strijk, J.S., Van Konijnenburg-van Cittert, J.H.A., Nucete, M. and Merckx, V.S.F.T.}, title = {Dated Phylogenies of the Sister Genera Macaranga and Mallotus (Euphorbiaceae): Congruence in Historical Biogeographic Patterns?}, journal = {PLoS ONE}, year = {2014}, number = {1}, volume = {9(1): e85713. doi: 10.1371/journal.pone.0085713}, pages = {e85713}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0085713} }
|Strijk, J.S., Bone, Thébaud, C., Buerki, S., Fritsch, P.W., Hodkinson, T.R. and Strasberg, D.
|Timing and tempo of evolutionary diversification in a biodiversity hotspot: Primulaceae on Indian Ocean islands.
|Journal of Biogeography
Vol. In Press, pp.
|Abstract:Aim We examined phylogenetic relationships and spatio-temporal diversification in Indian Ocean Primulaceae, assessing correlations between speciation rates, geographical expansion and ecomorphological specialization. Location Madagascar and Indian Ocean Islands. Methods We conducted phylogenetic analyses with plastid and nuclear DNA sequences of Primulaceae using maximum likelihood and Bayesian algorithms, and estimated divergence times using a Bayesian relaxed molecular clock. Temporal changes in diversification rate and possible correlations with the biogeographical history of the group were examined. We performed parametric ancestral area reconstruction incorporating a stratified palaeogeographical model that reflects changes in terrestrial configuration and the presence of phytogeographical connections through time in the western Indian Ocean Basin. Shifts in diversification rate were compared with ancestral area assignments and divergence age estimates. Results Indian Ocean Primulaceae were recovered as monophyletic with a sister relationship to Asian Ardisia. Oncostemum, a genus confined to Madagascar and the Comoros, was resolved as paraphyletic by the inclusion of a monophyletic Mascarene Badula group consisting of single-island endemics. We found evidence for diversification bursts early in the history of Indian Ocean Primulaceae that correspond closely to the sequence of dispersal and the appearance of newly formed Mascarene Islands. Age estimates suggest a dispersal to Rodrigues that is older than the estimated geological age of the island. Main conclusions Results suggest a Madagascan origin of Indian Ocean Primulaceae with subsequent dispersal to the Mascarenes in the middle to late Miocene, with initial establishment on either Mauritius or Rodrigues and subsequent stepping-stone dispersal to the other two Mascarene islands within the last 2 Myr. Analyses suggest that diversification has slowed over time, with significant rate changes following dispersal to new geographical areas. Onset of diversification in species-rich Oncostemum appears to have been recent, with major cladogenesis commencing in the early Pliocene.
@article{Strijk2013, author = {Strijk, J.S., Bone, Thébaud, C., Buerki, S., Fritsch, P.W., Hodkinson, T.R. and Strasberg, D.}, title = {Timing and tempo of evolutionary diversification in a biodiversity hotspot: Primulaceae on Indian Ocean islands.}, journal = {Journal of Biogeography}, year = {2013}, volume = {In Press}, url = {http://onlinelibrary.wiley.com/doi/10.1111/jbi.12259/abstract} }
|Zhai, De-Li and Xu, Jian-Chu and Dai, Zhi-Cong and Cannon, Charles H. and Grumbine, R.E.
|Increasing tree cover but losing diverse natural forests in Hainan, China
|Regional Environmental Change
|Abstract:To protect biodiversity and improve environmental conditions, China has invested billions of dollars in reforestation and payments for ecosystem service programs. Here, we examine the Sloping Land Conversion Program, the largest such program in the world and found that after 13 years of implementation at our study site, it has had negative impacts on natural tropical forests. GIS and remote sensing techniques revealed that both natural forests and natural shrub and grasslands were replaced by non-native monocultural plantations on Hainan Island, China, a key tropical biodiversity hotspot. Under current Chinese policy, these plantations are classified simply as "forests", with the assumption that they are equivalent to natural forests. This lack of a distinction in forest quality has led to substantial deforestation and plantation expansion, including encroachment into protected areas on Hainan. Additional social and economic drivers of these changes were identified by examining the participants in this program and their actions. Without a new ecologically based definition of forests and new goals for reforestation, such programs designed to improve ecosystem services, and forest quality may actually threaten remaining natural forests and other vegetation types in Hainan and in other areas of mainland China.
@article{Zhai2013, author = {Zhai, De-Li and Xu, Jian-Chu and Dai, Zhi-Cong and Cannon, Charles H. and Grumbine, R.E.}, title = {Increasing tree cover but losing diverse natural forests in Hainan, China}, journal = {Regional Environmental Change}, year = {2013}, }
|BONE, RUTH E. and STRIJK, JOERI S. and FRITSCH, PETER W. and BUERKI, SVEN and STRASBERG, DOMINIQUE and THÉBAUD, CHRISTOPHE and HODKINSON, TREVOR R.
|Phylogenetic inference of Badula (Primulaceae), a rare and threatened genus endemic to the Mascarene Archipelago
|Botanical Journal of the Linnean Society
|Abstract:With 14 species, Badula (Primulaceae) is the most species-rich endemic angiosperm genus of the Mascarene Archipelago. The relationship between Badula and its ally Oncostemum (c. 100 spp; Madagascar and the Comoros Islands) is uncertain, with implications for the circumscription of Badula as a Mascarene endemic. Within Badula, species rarity (several being critically endangered) and a paucity of herbarium specimens hamper proper species delimitations. Here, we estimate the phylogenetic relationships of Badula based on DNA sequence data from the nuclear ribosomal internal transcribed spacer (ITS) and plastid trnS-trnG-trnG regions with complete taxon sampling of the genus and three samples or more of each taxon. The results strongly supported the monophyly of Badula. Paraphyly of Oncostemum was inferred with weak support; explicit hypothesis testing did not favour this hypothesis over one that forced the monophyly of Oncostemum. Monophyly of several Badula spp. was supported, particularly for taxa from the older islands of Mauritius and Rodrigues. Badula is inferred to have reached the Mascarene Archipelago through a single colonization event. The majority of species segregated into island clades, implying that few, rather than multiple, colonization events have occurred in Badula among the islands of the archipelago.
@article{BONE2012, author = {BONE, RUTH E. and STRIJK, JOERI S. and FRITSCH, PETER W. and BUERKI, SVEN and STRASBERG, DOMINIQUE and THÉBAUD, CHRISTOPHE and HODKINSON, TREVOR R. }, title = {Phylogenetic inference of Badula (Primulaceae), a rare and threatened genus endemic to the Mascarene Archipelago }, journal = {Botanical Journal of the Linnean Society}, year = {2012}, }
|Cannon, C.H.
|A Curiosity moment for tropical biology?
Vol. 338, pp. 467
|Abstract:Letter to the editor.
@article{Cannon2012a, author = {Cannon, C.H.}, title = {A Curiosity moment for tropical biology?}, journal = {Science}, year = {2012}, volume = {338}, pages = {467}, url = {http://www.sciencemag.org/content/338/6106/467.1.citation} }
|Cannon, Charles H. and Harrison, Rhett and Qie, Lan and Slik, J.W. Ferry and Chen, Jin
|A proposal for expanding capacity for conservation science education in the tropical Asia-Pacific region
|Biology International
Vol. 50, pp. 85-94
|Abstract:Conservation science in the tropical Asia-Pacific region confronts a wide range of challenges that go far beyond the basic issues of conservation or science. These challenges have many dimensions: biogeographic, cultural, linguistic, political, and religious. The region has no unifying language or culture. While the general high level of endemism and complex biogeography is well known, particularly in the archipelago, the anthropogenic differences among neighboring countries can also be quite profound. Because the region hosts such a phenomenal diversity of biology and humanity, conservation biologists working there need a unique set of skills to navigate these many challenges. The Program for Field Studies at the Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences has initiated a set of courses aimed at graduate students in the region to foster the development of a regional network of young scientists. Direct interaction and collaboration during international field courses among students from the many countries of the region is an effective way to create such a network. We hope that the PFS office can serve as an impetus for the growth of a consortium of international courses that can bring together the many experts and institutions to inspire and educate the enthusiastic spirit of the young conservation biologists in the region.
@article{Cannon2012, author = {Cannon, Charles H. and Harrison, Rhett and Qie, Lan and Slik, J.W. Ferry and Chen, Jin}, title = {A proposal for expanding capacity for conservation science education in the tropical Asia-Pacific region}, journal = {Biology International}, year = {2012}, volume = {50}, pages = {85-94}, url = {http://biologyinternational.org/volume-50/} }
|Chen, X. and Cannon, Charles H. and Conklin-Brittan, N.L.
|Evidence for a trade-off strategy in stone oak (Lithocarpus) seeds between physical and chemical defense highlights fiber as an important antifeedant
|PLoS ONE
Vol. 7, pp. e32890
|Abstract:Trees in the beech or oak family (Fagaceae) have a mutualistic relationship with scatter-hoarding rodents. Rodents obtain nutrients and energy by consuming seeds, while providing seed dispersal for the tree by allowing some cached seeds to germinate. Seed predation and caching behavior of rodents is primarily affected by seed size, mechanical protection, macronutrient content, and chemical antifeedants. To enhance seed dispersal, trees must optimize trade-offs in investment between macronutrients and antifeedants. Here, we examine this important chemical balance in the seeds of tropical stone oak species with two substantially different fruit morphologies. These two distinct fruit morphologies in Lithocarpus differ in the degree of mechanical protection of the seed. For 'acorn' fruit, a thin exocarp forms a shell around the seed while for 'enclosed receptacle' (ER) fruit, the seed is embedded in a woody receptacle. We compared the chemical composition of numerous macronutrient and antifeedant in seeds from several Lithocarpus species, focusing on two pairs of sympatric species with different fruit morphologies. We found that macronutrients, particularly total non-structural carbohydrate, was more concentrated in seeds of ER fruits while antifeedants, primarily fibers, were more concentrated in seeds of acorn fruits. The trade-off in these two major chemical components was more evident between the two sympatric lowland species than between two highland species. Surprisingly, no significant difference in overall tannin concentrations in the seeds was observed between the two fruit morphologies. Instead, the major trade-off between macronutrients and antifeedants involved indigestible fibers. Future studies of this complex mutualism should carefully consider the role of indigestible fibers in the foraging behavior of scatter-hoarding rodents.
@article{Chen2012, author = {Chen, X. and Cannon, Charles H. and Conklin-Brittan, N.L.}, title = {Evidence for a trade-off strategy in stone oak (Lithocarpus) seeds between physical and chemical defense highlights fiber as an important antifeedant}, journal = {PLoS ONE}, year = {2012}, number = {3}, volume = {7}, pages = {e32890}, }
|Kua, C.S. and Ruan, J. and Harting, J. and Ye, C.X. and Helmus, M.R. and Yu J. and Cannon, C.H.
|Reference-free comparative genomics of 174 chloroplasts
|PLoS One
Vol. 7, pp. e48995
|Abstract:Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ,18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid [2] to a massive algal chloroplast [3], including gnetophytes [4] and cycads [5]. The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied genomes and rapid discovery of informative candidate regions.
@article{Kua2012, author = {Kua, C.S. and Ruan, J. and Harting, J. and Ye, C.X. and Helmus, M.R. and Yu J. and Cannon, C.H.}, title = {Reference-free comparative genomics of 174 chloroplasts}, journal = {PLoS One}, year = {2012}, number = {11}, volume = {7}, pages = {e48995}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048995} }
|Strijk, Joeri S. and Noyes, Richard D. and Strasberg, Dominique and Cruaud, Corinne and Gavory, Fredéric and Chase, Mark W. and Abbott, Richard J. and Thébaud, Christophe
|In and out of Madagascar: Dispersal to Peripheral Islands, Insular Speciation and Diversification of Indian Ocean Daisy Trees (Psiadia, Asteraceae)
|PLoS ONE
|Abstract:Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.
@article{Strijk2012, author = {Strijk, Joeri S. and Noyes, Richard D. and Strasberg, Dominique and Cruaud, Corinne and Gavory, Fredéric and Chase, Mark W. and Abbott, Richard J. and Thébaud, Christophe }, title = {In and out of Madagascar: Dispersal to Peripheral Islands, Insular Speciation and Diversification of Indian Ocean Daisy Trees (Psiadia, Asteraceae)}, journal = {PLoS ONE}, year = {2012}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0042932?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+plosone%2FPLoSONE+%28PLoS+ONE+Alerts%3A+New+Articles%29} }
|Ye, Cheng Xi and Ma, Zhangshan S and Cannon, Charles H. and Yu, Douglas W.
|Exploiting sparseness in de novo genome assembly
|BMC Bioinformatics
Vol. 13, pp. S1
|Abstract:Background The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. Methods In 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. Results We 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.
@article{Ye2012, author = {Ye, Cheng Xi and Ma, Zhangshan S and Cannon, Charles H. and Yu, Douglas W.}, title = {Exploiting sparseness in de novo genome assembly}, journal = {BMC Bioinformatics}, year = {2012}, number = {S6}, volume = {13}, pages = {S1}, }
|Zhai, De-Li and Cannon, Charles H. and Slik, J.W. Ferry and Zhang, Cui-Pang and Dai, Zhi-Cong
|Rubber and pulp plantations represent a double threat to Hainan's natural tropical forests
|Journal of Environmental Management
Vol. 96, pp. 64-73
|Abstract: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 Hainan's 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 (979e1040 sq km) but decreased rapidly (763 sq km) over the next decade. Rubber plantations increased steadily through the study period while pulp plantations appeared after 1995 but occupied 152 sq km 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 pre- venting forest conversion on marginal and protected areas.
@article{Zhai2012, author = {Zhai, De-Li and Cannon, Charles H. and Slik, J.W. Ferry and Zhang, Cui-Pang and Dai, Zhi-Cong}, title = {Rubber and pulp plantations represent a double threat to Hainan's natural tropical forests}, journal = {Journal of Environmental Management}, year = {2012}, volume = {96}, pages = {64-73}, }
|Cannon, Charles H. and Chen, X.
|Lithocarpus pulongtauensis (Fagaceae), a new species from Borneo
|Annales Botanica Fennici
Vol. 48, pp.
|Abstract: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.
@article{Cannon2011, author = {Cannon, Charles H. and Chen, X.}, title = {Lithocarpus pulongtauensis (Fagaceae), a new species from Borneo }, journal = {Annales Botanica Fennici}, year = {2011}, volume = {48}, }
|Kettle, Chris J. and Cannon, Charles H. and 26 others
|Seeing the fruit for the trees
|Conservation Letters
Vol. 4, pp. 184–191
|Abstract:The recent mass fruiting of forest trees in Borneo is an urgent wakeup call: existing policy instruments, financial mechanisms, and forestry infrastructure are inadequate to take full advantage of these infrequent opportunities for forest restoration and conservation. Tropical forest restoration can provide substantial benefits for biodiversity conservation, climate change mitigation, and poverty alleviation. Yet the unpredictability of the synchronized flowering and consequent mass fruiting of many forest trees in Borneo presents a distinctive set of challenges for forest restoration. Significant financing and a considerable coordinated effort are required to prepare for future mass fruiting events if we are to capitalize on opportunities for ecological restoration. The continued high rate of forest clearance in this region and the rarity of mass fruiting events suggest that there may be few remaining opportunities to prevent widespread species extinctions. In this article we propose a facilitatory policy framework for forest restoration in Borneo to stimulate action in advance of the next mass fruiting of forest trees.
@article{Kettle2011, author = {Kettle, Chris J. and Cannon, Charles H. and 26 others}, title = {Seeing the fruit for the trees}, journal = {Conservation Letters}, year = {2011}, number = {3}, volume = {4}, pages = {184–191}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1755-263X.2010.00161.x/abstract} }
|Liu, S. and Cannon, Charles H.
|Impact of socio-economic status on the implementation of China's collective forest tenure reform in Zhang Guying Township, Hunan: potential for increasing disparity
Vol. 84, pp.
|Abstract:China's collective forest tenure reform will have a profound impact on the livelihoods of rural people. For the equitable implementation of reform, rural smallholders need sufficient knowledge and understanding of the opportunities and limitations offered by reform. Here, we examine rural smallholder's awareness and attitude towards the reform, across the socio-economic range, in three villages of Zhang Guying Township, Hunan province. Income level and educational background played a consistent role in knowledge and understanding of the reform, as people with low income and no formal education were more likely to be unaware and have no clear understanding of the reform. Additionally, low -income rural smallholders were more likely to convert forest to cash crops, undercutting the central government's stated objectives for the forest reform to improve forest condition. Given our results, the government needs to ensure equitable distribution of information, specifically targeting low-income villagers without formal education. The strong disparity in knowledge and understanding between wealthy and poor creates a situation where the wealthy effectively benefit from the reform, while the poor miss its opportunity. This inequality has great potential for generating future unrest and conflict and for damaging forest condition due to unsustainable or uninformed practices.
@article{Liu2011, author = {Liu, S. and Cannon, Charles H.}, title = {Impact of socio-economic status on the implementation of China's collective forest tenure reform in Zhang Guying Township, Hunan: potential for increasing disparity }, journal = {Forestry}, year = {2011}, number = {3}, volume = {84}, }
|Slik, J.W. Ferry adn van Beek, M. and Bernard, C. and Bongers, F. and Breman, F.C. and Cannon, C.H. and Sidiyasa, K.
|Limited edge effects along a burned-unburned Bornean forest boundary seven years after disturbance
Vol. 43, pp. 288-298
|Abstract:Large parts of the everwet tropics have been burned, leaving many unburned–burned forest edges. Here we studied a Bornean forest edge to determine: (1) how unburned and burned forest differ in vegetation structure, diversity, composition and plant functional traits 7 yr after fire, and (2) if these variables showed significant edge effects. Environmental and inventory data from 120 plots (0.01 ha each), covering both sides of a $1.3 km forest boundary were sampled. Differences in vegetation structure, diversity, composition and plant functional traits were analyzed in relation to disturbance type (Mann–Whitney tests) and edge distance (partial correlation analysis that controlled for confounding effects of elevation, slope and fire intensity). Seven years after fire, burned forest differed significantly from unburned forest in most measured variables while few significant edge effects were detected, i.e., there existed a sharp delimitation between the two forest types. The regeneration of the burned forest depended almost entirely on in situ recruitment with little input of late successional species from the neighboring old growth forest. On the other hand, old growth forest showed few signs of edge degradation. A possible explanation for these results might be related to the absence of a mast fruiting event during these first 7 yr of forest recovery, resulting in low levels of late successional species seed input into the burned forest, combined with the quick development of a closed canopy in the burned forest by early successional species that shielded the unburned forest from adverse edge effects.
@article{Slik2011a, author = {Slik, J.W. Ferry adn van Beek, M. and Bernard, C. and Bongers, F. and Breman, F.C. and Cannon, C.H. and Sidiyasa, K.}, title = {Limited edge effects along a burned-unburned Bornean forest boundary seven years after disturbance}, journal = {Biotropica}, year = {2011}, number = {3}, volume = {43}, pages = {288-298}, }
|Slik, J.W. Ferry and Cannon, Charles H. and 29 others
|Soils on exposed Sunda Shelf shaped biogeographic patterns in the equatorial forests of Southeast Asia
|Proceedings of National Academy of Sciences (U.S.A.)
Vol. 108, pp. 12343-12347
|Abstract:The marked biogeographic difference between western (Malay Peninsula and Sumatra) and eastern (Borneo) Sundaland is surpris- ing given the long time that these areas have formed a single landmass. A dispersal barrier in the form of a dry savanna corridor during glacial maxima has been proposed to explain this disparity. However, the short duration of these dry savanna conditions make it an unlikely sole cause for the biogeographic pattern. An addi- tional explanation might be related to the coarse sandy soils of central Sundaland. To test these two nonexclusive hypotheses, we performed a floristic cluster analysis based on 111 tree inven- tories from Peninsular Malaysia, Sumatra, and Borneo. We then identified the indicator genera for clusters that crossed the central Sundaland biogeographic boundary and those that did not cross and tested whether drought and coarse-soil tolerance of the indi- cator genera differed between them. We found 11 terminal floristic clusters, 10 occurring in Borneo, 5 in Sumatra, and 3 in Peninsular Malaysia. Indicator taxa of clusters that occurred across Sundaland had significantly higher coarse-soil tolerance than did those from clusters that occurred east or west of central Sundaland. For drought tolerance, no such pattern was detected. These results strongly suggest that exposed sandy sea-bed soils acted as a dis- persal barrier in central Sundaland. However, we could not confirm the presence of a savanna corridor. This finding makes it clear that proposed biogeographic explanations for plant and animal distri- butions within Sundaland, including possible migration routes for early humans, need to be reevaluated.
@article{Slik2011, author = {Slik, J.W. Ferry and Cannon, Charles H. and 29 others}, title = {Soils on exposed Sunda Shelf shaped biogeographic patterns in the equatorial forests of Southeast Asia}, journal = {Proceedings of National Academy of Sciences (U.S.A.)}, year = {2011}, number = {30}, volume = {108}, pages = {12343-12347}, }
|Wong, M.M.L. and Cannon, Charles H. and Wickneswari, Ratnam
|Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing
|BMC Genomics
Vol. 12, pp. 01-13
|Abstract:Abstract Background: Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well- characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants. Results: We sequenced transcriptomes of A. auriculiformis and A. mangium from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. De novo assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for A. auriculiformis and A. mangium respectively. The assemblies of A. auriculiformis and A. mangium had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3-MYB proteins in other plant species that are involved in transcriptional regulation of secondary cell wall formation and lignin deposition. We searched the contigs against public microRNA database and predicted the stem-loop structures of six highly conserved microRNA families (miR319, miR396, miR160, miR172, miR162 and miR168) and one legume-specific family (miR2086). Three microRNA target genes were predicted to be involved in wood formation and flavonoid biosynthesis. By using the assemblies as a reference, we discovered 16,648 and 9,335 high quality putative Single Nucleotide Polymorphisms (SNPs) in the transcriptomes of A. auriculiformis and A. mangium, respectively, thus yielding useful markers for population genetics studies and marker-assisted selection. Conclusion: We have produced the first comprehensive transcriptome-wide analysis in A. auriculiformis and A. mangium using de novo assembly techniques. Our high quality and comprehensive assemblies allowed the identification of many genes in the lignin biosynthesis and secondary cell wall formation in Acacia hybrids. Our results demonstrated that Next Generation Sequencing is a cost-effective method for gene discovery, identification of regulatory sequences, and informative markers in a non-model plant.
@article{Wong, author = {Wong, M.M.L. and Cannon, Charles H. and Wickneswari, Ratnam}, title = {Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing }, journal = {BMC Genomics}, year = {2011}, number = {342}, volume = {12}, pages = {01-13}, url = {http://www.biomedcentral.com/1471-2164/12/342 } }
|Zhang, L. and Li, H.T. and Gao, L.M. and Yang, J.B. and Li, D.Z. and Cannon, C.H. and Chen, J. and Li, Q.J.
|Phylogeny and evolution of bracts and bracteoles in Tacca (Dioscoreaceae)
|Journal of Integrative Plant Biology
|Abstract:Most species in the genus Tacca (Dioscoreaceae) feature green to black purple, conspicuous inflores- cence involucral bracts with variable shapes, motile filiform appendages (bracteoles), and diverse types of inflorescence morphology. To infer the evolution of these inflorescence traits, we reconstructed the molecular phylogeny of the genus, using DNA sequences from one nuclear, one mitochondrial, and three plastid loci (Internal Transcribed Spacer (ITS), atpA, rbcL, trnL-F, and trnH-psbA). Involucres and bracteoles characters were mapped onto the phylogeny to analyze the sequence of inflorescence trait evolution. In all analyses, species with showy involucres and bracteoles formed the most derived clade, while ancestral Tacca had small and plain involucres and short bracteoles, namely less conspicuous inflorescence structures. Two of the species with the most elaborate inflorescence morphologies (T. chantrieri in southeast China and T. integrifolia in Tibet), are predominantly self-pollinated, indicating that these conspicuous floral displays have other functions rather than pollinator attraction. We hypothesize that the motile bracteoles and involucres may facilitate selfing; display photosynthesis in the dim understory, and protect flowers from herbivory.
@article{Zhang2011, author = {Zhang, L. and Li, H.T. and Gao, L.M. and Yang, J.B. and Li, D.Z. and Cannon, C.H. and Chen, J. and Li, Q.J.}, title = {Phylogeny and evolution of bracts and bracteoles in Tacca (Dioscoreaceae)}, journal = {Journal of Integrative Plant Biology}, year = {2011}, }
|Cannon, C.H. and Kua, C.S. and Zhang, D. and Harting, J.R.
|Assembly-free comparative genomics of short-read sequence data discovers the needle in the haystack
|Molecular Ecology
Vol. 19, pp. 146-160
@article{Cannon2010, author = {Cannon, C.H. and Kua, C.S. and Zhang, D. and Harting, J.R.}, title = {Assembly-free comparative genomics of short-read sequence data discovers the needle in the haystack}, journal = {Molecular Ecology}, year = {2010}, volume = {19}, pages = {146-160}, }
|Helmus, M. R. and Keller, W. and Paterson, M. J. and Yan, N. D. and Cannon, C. H. and Rusak, J. A.
|Communities contain closely related species during ecosystem disturbance
|Ecology Letters
Vol. 13, pp. 162-174
|Abstract: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.
@article{Helmus2010, author = {Helmus, M. R. and Keller, W. and Paterson, M. J. and Yan, N. D. and Cannon, C. H. and Rusak, J. A.}, title = {Communities contain closely related species during ecosystem disturbance}, journal = {Ecology Letters}, year = {2010}, number = {2}, volume = {13}, pages = {162-174}, }
|Kembel, S. W. and Cowan, P. D. and Helmus, M. R. and Cornwell, W. K. and Morlon, H. and Ackerly, D. D. and Blomberg, S. P. and Webb, C. O.
|Picante: R tools for integrating phylogenies and ecology
Vol. 26, pp. 1463-1464
@article{Kembel2010, author = {Kembel, S. W. and Cowan, P. D. and Helmus, M. R. and Cornwell, W. K. and Morlon, H. and Ackerly, D. D. and Blomberg, S. P. and Webb, C. O.}, title = {Picante: R tools for integrating phylogenies and ecology}, journal = {Bioinformatics}, year = {2010}, volume = {26}, pages = {1463-1464}, }
|Kettle, Chris J. and Cannon, Charles H. and 26 others
|Mass fruiting in Borneo: a missed opportunity
Vol. 330, pp. 584
@article{Kettle2010, author = {Kettle, Chris J. and Cannon, Charles H. and 26 others}, title = {Mass fruiting in Borneo: a missed opportunity}, journal = {Science}, year = {2010}, volume = {330}, pages = {584}, }
|Slik J.W.F., S.I. Aiba, F.Q. Brearley, C.H. Cannon, O. Forshed, K. Kitayama, H. Nagamasu, R. Nilus, J. Payne, G. Paoli, A. Poulsen, N. Raes, D. Sheil, K. Sidiyasa, E. Suzuki, J.L.C.H. van Valkenburg
|Environmental correlates for tree biomass, basal area, wood specific gravity and stem density gradients in Borneo's tropical forests.
|Global Ecology and Biogeography
Vol. 19, pp. 50-60
|Abstract:Aim Tropical forests have been recognized as important global carbon sinks and sources. However, many uncertainties about the spatial distribution of live tree above-ground biomass (AGB) remain, mostly due to limited availability of AGB field data. Recent studies in the Amazon have already shown the importance of large sample size for accurate AGB gradient analysis. Here we use a large stem density, basal area, community wood density and AGB dataset to study and explain their spatial patterns in an Asian tropical forest. Location Borneo, Southeast Asia. Methods We combined stem density, basal area, community wood density and AGB data from 83 locations in Borneo with an environmental database containing elevation, climate and soil variables. The Akaike information criterion was used to select models and environmental variables that best explained the observed values of stem density, basal area, community wood density and AGB. These models were used to extrapolate these parameters across Borneo. Results We found that wood density, stem density, basal area and AGB respond significantly, but differentially, to the environment. AGB was only correlated with basal area, but not with stem density and community wood specific gravity. Main conclusions Unlike results from Amazonian forests, soil fertility was an important positive correlate for AGB in Borneo while community wood density, which is a main driver of AGB in the Neotropics, did not correlate with AGB in Borneo. Also, Borneo's average AGB of 457.1 Mg ha-1 was c. 60% higher than the Amazonian average of 288.6 Mg ha-1.We find evidence that this difference might be partly explained by the high density of large wind-dispersed Dipterocarpaceae in Borneo, which need to be tall and emergent to disperse their seeds. Our results emphasize the importance of Bornean forests as carbon sinks and sources due to their high carbon storage capacity.
@article{Slik2010, author = {Slik J.W.F., S.I. Aiba, F.Q. Brearley, C.H. Cannon, O. Forshed, K. Kitayama, H. Nagamasu, R. Nilus, J. Payne, G. Paoli, A. Poulsen, N. Raes, D. Sheil, K. Sidiyasa, E. Suzuki, J.L.C.H. van Valkenburg}, title = {Environmental correlates for tree biomass, basal area, wood specific gravity and stem density gradients in Borneo's tropical forests.}, journal = {Global Ecology and Biogeography}, year = {2010}, volume = {19}, pages = {50-60}, }
|Slik, J. W. F. and Breman, F. C. and Bernard, C. and van Beek, M. and Cannon, C. H. and Eichhorn, K. A. O. and Sidiyasa, K.
|Fire as a selective force in a Bornean tropical everwet forest
Vol. 164, pp. 841-849
@article{Slik2010a, author = {Slik, J. W. F. and Breman, F. C. and Bernard, C. and van Beek, M. and Cannon, C. H. and Eichhorn, K. A. O. and Sidiyasa, K.}, title = {Fire as a selective force in a Bornean tropical everwet forest}, journal = {Oecologia}, year = {2010}, volume = {164}, pages = {841-849}, }
|Webb, C.O., J.W.F. Slik, T. Triono
|Biodiversity inventory and informatics in Southeast Asia.
|Biodiversity and Conservation
|Abstract:Rapidly changing land use in Southeast Asia threatens plant diversity, and reduces the time we have left to document it. Despite over 200 years of scientific plant exploration, many plant species have yet to be discovered. Moreover, we still have a very poor understanding of the distribution of known taxa in this biogeographically complex region. We review the current state of biodiversity exploration, using plants in Indonesia as an example. Traditional methods of collecting and describing species have provided a solid foundation for our understanding of plant biodiversity, but are insufficient for the pragmatic task of rapidly discovering and documenting today's biodiversity before it is gone, because general collecting expeditions tend to be infrequent, and documentation of most new species must await taxonomic revisions many years in the future. Solutions to this exploration and documentation crisis (i) could use the abundant resource of enthusiastic, networked, national biology students, (ii) should employ biodiversity informatics tools to efficiently engage both specialists and parataxonomists, and (iii) might require adoption of new types of a-taxonomy, utilizing increasingly low-cost molecular methods and high resolution photographs. We describe emerging technologies that will facilitate this taxonomic development. We believe that a new golden age of biodiversity exploration may be dawning, just as biodiversity itself is most threatened, and are hopeful that increasing knowledge of biodiversity will be a positive force to slow its loss.
@article{Webb2010, author = {Webb, C.O., J.W.F. Slik, T. Triono}, title = {Biodiversity inventory and informatics in Southeast Asia.}, journal = {Biodiversity and Conservation}, year = {2010}, }
|Ahrenstorff, Tyler D. and Sass, Greg G. and Helmus, Matthew R.
|The influence of littoral zone coarse woody habitat on home range size, spatial distribution, and feeding ecology of largemouth bass (Micropterus salmoides)
Vol. 623, pp.
|Abstract:Abstract Coarse woody habitat (CWH) may be a critical feature of lakes that influences fish distribu-tions, movement patterns, and feeding habits. We used radio telemetry to examine the role of CWH in determining the movements of largemouth bass (Micropterus salmoides Lacepede) in the context of two whole-lake experiments that provided a gradient of four lake basins varying in natural and manipu- lated CWH. We also conducted diet studies on largemouth bass in these lakes to test for correlates among consumption rate and prey selectivity with bass behavior. Our results indicated that largemouth bass in basins with lower CWH abundances had larger home ranges, spent more time in deep water, were more selective predators, and showed lower consumption rates. Largemouth bass in basins with higher CWH abundances showed the opposite patterns. Low CWH abundances were correlated with a shift in largemouth bass foraging behavior from sit-and-wait to actively searching. This increased activity, coupled with the potential decline of prey fish species in the absence of CWH, may decrease largemouth bass growth potential regardless of the prey type consumed. Our results suggest that lake-shore residential development and associated removals of CWH from lakes may influence fish behavior, while CWH augmentation may reverse some of those changes.
@article{Ahrenstorff2009, author = {Ahrenstorff, Tyler D. and Sass, Greg G. and Helmus, Matthew R.}, title = {The influence of littoral zone coarse woody habitat on home range size, spatial distribution, and feeding ecology of largemouth bass (Micropterus salmoides)}, journal = {Hydrobiologia}, year = {2009}, number = {1}, volume = {623}, }
|Cannon, C.H. and Morley, R.J. and Bush, A.B.G.
|The current refugial rainforests of Sundaland are unrepresentative of their biogeographic past and highly vulnerable to disturbance
|Proceedings Of The National Academy Of Sciences Of The United States Of America
Vol. 106, pp. 11188-11193
|Abstract:Understanding the historical dynamics of forest communities is a critical element for accurate prediction of their response to future change. Here, we examine evergreen rainforest distribution in the Sunda Shelf region at the last glacial maximum (LGM), using a spatially explicit model incorporating geographic, paleoclimatic, and geologic evidence. Results indicate that at the LGM, Sundaland rainforests covered a substantially larger area than currently present. Extrapolation of the model over the past million years demonstrates that the current "island archipelago'' setting in Sundaland is extremely unusual given the majority of its history and the dramatic biogeographic transitions caused by global de-glaciation were rapid and brief. Compared with dominant glacial conditions, lowland forests were probably reduced from approximately 1.3 to 0.8 x 10(6) km(2) while upland forests were probably reduced by half, from approximately 2.0 to 1.0 x 105 km(2). Coastal mangrove and swamp forests experienced the most dramatic change during deglaciations, going through a complete and major biogeographic relocation. The Sundaland forest dynamics of fragmentation and contraction and subsequent expansion, driven by glacial cycles, occur in the opposite phase as those in the northern hemisphere and equatorial Africa, indicating that Sundaland evergreen rainforest communities are currently in a refugial stage. Widespread human-mediated reduction and conversion of these forests in their refugial stage, when most species are passing through significant population bottlenecks, strongly emphasizes the urgency of conservation and management efforts. Further research into the natural process of fragmentation and contraction during deglaciation is necessary to understand the long-term effect of human activity on forest species.
@article{Cannon2009, author = {Cannon, C.H. and Morley, R.J. and Bush, A.B.G.}, title = {The current refugial rainforests of Sundaland are unrepresentative of their biogeographic past and highly vulnerable to disturbance}, journal = {Proceedings Of The National Academy Of Sciences Of The United States Of America}, year = {2009}, number = {27}, volume = {106}, pages = {11188-11193}, url = {http://www.pnas.org/content/106/27/11188} }
|Chen, J. and Cannon, C. H. and Hu, H. B.
|Tropical botanical gardens: at the in situ ecosystem management frontier
|Trends In Plant Science
Vol. 14, pp. 584-589
|Abstract: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.
@article{Chen2009, author = {Chen, J. and Cannon, C. H. and Hu, H. B.}, title = {Tropical botanical gardens: at the in situ ecosystem management frontier}, journal = {Trends In Plant Science}, year = {2009}, number = {11}, volume = {14}, pages = {584-589}, }
|Raes N, MC Roos, JWF Slik, EE van Loon, H ter Steege
|Botanical richness and endemicity patterns of Borneo derived from species distribution models
Vol. 32, pp. 180-192
|Abstract:This study provides a Borneo-wide, quantitative assessment of botanical richness and endemicity at a high spatial resolution, and based on actual collection data. To overcome the bias in collection effort, and to be able to predict the presence and absence of species, even for areas where no collections have been made, we constructed species distribution models (SDMs) for all species taxonomically revised in Flora Malesiana. Species richness and endemicity maps were based on 1439 significant SDMs. Mapping of the residuals of the richness-endemicity relationship identified areas with higher levels of endemicity than can be expected on the basis of species richness, the endemicity hotspots. We were able to identify one previously unknown region of high diversity, the high mountain peaks of East Kalimantan; and two additional endemicity hotspots, the Mu¨ller Mountains and the Sangkulirang peninsula. The areas of high diversity and endemicity were characterized by a relatively small range in annual temperature, but with seasonality in temperatures within that range. Furthermore, these areas were least affected by El Nino Southern Oscillation drought events. The endemicity hotspots were found in areas, which were ecologically distinct in altitude, edaphic conditions, annual precipitation, or a combination of these factors. These results can be used to guide conservation efforts of the highly threatened forests of Borneo.
@article{Raes2009, author = {Raes N, MC Roos, JWF Slik, EE van Loon, H ter Steege}, title = {Botanical richness and endemicity patterns of Borneo derived from species distribution models}, journal = {Ecography}, year = {2009}, volume = {32}, pages = {180-192}, }
|Slik JWF, N Raes, SI Aiba, FQ Brearley, CH Cannon, E Meijaard, H Nagamasu, R Nilus, G Paoli, AD Poulsen, D Sheil, E Suzuki, JLCH van Valkenburg, CO Webb, P Wilkie, S Wulffraat
|Environmental correlates for tropical tree diversity and distribution patterns in Borneo
|Diversity and Distributions
Vol. 15, pp. 523-532
|Abstract:Aim Identify environmental correlates for tropical tree diversity and composition. Location Borneo, Southeast Asia. Methods A GIS-environmental database with 5 arc minute (c. 10×10 km) resolution was combined with tree inventory data. Tree diversity, phylogenetic diversity (PD) and the two main compositional gradients were determined for 46 tree inventories. Akaike's information criterion and a data jackknifing procedure were used to select 50 explanatory models for diversity and composition gradients. The average of these models was used as our final diversity and compositional model. We applied Moran's I to detect spatial autocorrelation of residuals. Results Tree diversity, PD and the two main compositional gradients in Borneo were all significantly correlated with the environment. Tree diversity correlated negatively with elevation, soil depth, soil coarseness (texture) and organic carbon content, whereas it correlated positively with soil C:N ratio, soil pH, moisture storage capacity and annual rainfall. Tree PD was correlated positively with elevation and temperature seasonality and was largely determined by gymnosperms. However, angiosperm PD also correlated positive with elevation. Compositional patterns were strongly correlated with elevation but soil texture, cation-exchange-capacity, C:N ratio, C and N content and drainage were also important next to rainfall seasonality and El Niño Southern Oscillation drought impact. Main conclusions Although elevation is the most important correlate for diversity and compositional gradients in Borneo, significant additional variability is explained by soil characteristics (texture, carbon content, pH, depth, drainage and nutrient status) and climate (annual rainfall, rainfall seasonality and droughts). The identified environmental correlates for diversity and composition gradients correspond to those found in other tropical regions of the world. Differences between the regions are mainly formed by differences in the relative importance of the environmental variables in explaining diversity and compositional gradients.
@article{Slik2009, author = {Slik JWF, N Raes, SI Aiba, FQ Brearley, CH Cannon, E Meijaard, H Nagamasu, R Nilus, G Paoli, AD Poulsen, D Sheil, E Suzuki, JLCH van Valkenburg, CO Webb, P Wilkie, S Wulffraat}, title = {Environmental correlates for tropical tree diversity and distribution patterns in Borneo}, journal = {Diversity and Distributions}, year = {2009}, volume = {15}, pages = {523-532}, }
|Welzen, P.C. van and J.W.F. Slik
|Patterns in species richness and composition of plant families in the Malay archipelago.
Vol. 54, pp. 166-171
|Abstract:Distribution patterns or the recognition of phytogeographical areas is usually based on the presence and absence of species. The taxa on which the analyses are based remain virtually anonymous. Here we want to determine which Malesian plant families (within the sample) are responsible for species richness and composition patterns. The other aim is to determine whether the different islands groups in Southeast Asia can be grouped into separate phytogeographical areas. A Principal Coordinates Analysis (PCO) showed the presence of three phytogeographical areas within Malesia: The Sunda Shelf (Malay Peninsula, Sumatra, Borneo) in the west, the Sahul Shelf (New Guinea) in the east, and all remaining central areas forming Wallacea. The latter can be divided into two parts (Java and the Lesser Sunda Islands versus the Philippines, Sulawesi and the Moluccas). Only twenty plant families (out of 164 sampled) account for most of the biodiversity on the island groups, both in total and endemic species numbers. These twenty families show a limited number of species richness patterns that are significantly associated with one or several of the detected phytogeographical areas. Only a few plant families were equally common throughout the whole Malesian region. Conservation efforts in Malesia should take this spatial distribution pattern into account in order to maximise preservation of both species diversity and complementarity.
@article{Welzen2009, author = {Welzen, P.C. van and J.W.F. Slik}, title = {Patterns in species richness and composition of plant families in the Malay archipelago.}, journal = {Blumea}, year = {2009}, volume = {54}, pages = {166-171}, }
|Helmus, Matthew R. and Allen, Lauren B. and Dominguez-Dominguez, Omar and Pardo, Edmundo Díaz and Gesundheit, Pablo and Lyons, John and Silva, Norman Mercado
|Threatened fishes of the world: Allotoca goslinei Smith and Miller, 1987 (Goodeidae)
|Environmental Biology of Fishes
Vol. 84, pp. 197-198
@article{Helmus2008a, author = {Helmus, Matthew R. and Allen, Lauren B. and Dominguez-Dominguez, Omar and Pardo, Edmundo Díaz and Gesundheit, Pablo and Lyons, John and Silva, Norman Mercado}, title = {Threatened fishes of the world: Allotoca goslinei Smith and Miller, 1987 (Goodeidae) }, journal = {Environmental Biology of Fishes}, year = {2008}, number = {2}, volume = {84}, pages = {197-198}, }
|The rapid effects of a whole-lake reduction of coarse woody debris on fish and benthic macroinvertebrates
|Freshwater Biology
Vol. 53, pp. 1423--1433
|Abstract:1. Ecosystems can enhance the biodiversity of adjacent ecosystems through subsidies of prey, nutrients and also habitat. For example, trees can fall into aquatic ecosystems and act as a subsidy that increases aquatic habitat heterogeneity. This habitat subsidy is vulnerable in lakes where anthropogenic development of shorelines coincides with a thinning of riparian forests and the removal of these dead trees (termed coarse woody debris: CWD). How the disruption of this subsidy affects lake ecosystems is not well understood. 2. We performed a whole ecosystem experiment on Little Rock Lake, a small (18 ha), undeveloped, and unfished lake in Vilas County, WI, U.S.A., that is divided into two similar-sized basins by a double poly-vinyl chloride curtain that prevents both fish and water exchange between basins. In 2002, we removed about 70% of the littoral CWD in the treatment basin, while the reference basin was left unaltered. We tested for changes in both fish and benthic macroinvertebrate community composition in the two years following the CWD reduction. 3. Yellow perch (Perca flavescens) was the most abundant fish species in the lake prior to our experiment, but declined to very low densities in the treatment basin after manipulation. We found no evidence of an effect on macroinvertebrates – the treatment basin's macroinvertebrate community composition, diversity and density did not change relative to the reference basin. 4. Our results indicate that different trophic groups may have differential responses to the loss of a habitat subsidy, even if anthropogenic effects on that subsidy are severe. In the case of Little Rock Lake, fish community responses were evident on a short-time scale, whereas the macroinvertebrate community did not rapidly change following CWD reduction.
@article{HELMUS2008, author = {HELMUS, MATTHEW R. AND SASS, GREG G.}, title = {The rapid effects of a whole-lake reduction of coarse woody debris on fish and benthic macroinvertebrates}, journal = {Freshwater Biology}, year = {2008}, number = {7}, volume = {53}, pages = {1423--1433}, }
|Manos, P.S. and Cannon, C.H. and Oh, S.H.
|Phylogenetic relationships and taxonomic status of the paleoendemic Fagaceae of Western North America: Recognition of a new genus, Notholithocarpus
Vol. 55, pp. 181-190
@article{Manos2008, author = {Manos, P.S. and Cannon, C.H. and Oh, S.H.}, title = {Phylogenetic relationships and taxonomic status of the paleoendemic Fagaceae of Western North America: Recognition of a new genus, Notholithocarpus}, journal = {Madrono}, year = {2008}, number = {3}, volume = {55}, pages = {181-190}, }
|Marshall, A.J. and Cannon, C. H. and Leighton, M.
|Competition and niche overlap between gibbons (Hylobates albibarbis) and other frugivorous vertebrates in Gunung Palung National Park, West Kalimantan, Indonesia
|The Gibbons: New Perspectives on Small Ape Socioecology and Population Biology
|Book Part
@incollection{Marshall2008, author = {Marshall, A.J. and Cannon, C. H. and Leighton, M.}, title = {Competition and niche overlap between gibbons (Hylobates albibarbis) and other frugivorous vertebrates in Gunung Palung National Park, West Kalimantan, Indonesia}, journal = {The Gibbons: New Perspectives on Small Ape Socioecology and Population Biology}, year = {2008}, pages = {--}, }
|Mercado-Silva, Norman and Helmus, Matthew R. and Vander Zanden, M. Jake
|The effects of impoundment and non-native species on a river food web in Mexico's central plateau
|River Research and Applications
|Abstract:Habitat modifications, non-native species and other anthropogenic impacts have restructured fish communities in lotic ecosystems of central Mexico. Conservation of native fishes requires understanding of food web changes resulting from the introduction of non-native species, flow alteration and other human impacts. Using 13C and 15N analysis of fishes and invertebrates we investigated the effects of non-native species, and reservoirs on food webs of the Laja river ecosystem (Guanajuato, central Mexico). We estimated trophic position (TP), relative trophic niche and food web dispersion at 11 reservoir, river and tailwater sites. Reservoirs and non-native fishes modified food webs in the Laja. Food web dispersion was greater in reservoir than in tailwater and river sites. Reservoir food webs had the greatest range of 13C values, indicating a more diverse resource base compared to rivers. 13C values increased with distance downstream from reservoirs, suggesting declining subsidies of river food webs by reservoir productivity. Stable isotopes revealed potential effects of non-native fishes on native fishes via predation or competition. Non-native Micropterus salmoides were top predators in the system. Non-natives Cyprinus carpio, Oreochromis mossambicus and Carassius auratus exhibited lowest TP in the Laja but overlapped significantly with most native species, indicating potential for resource competition. Native Chirostoma jordani was the only species with a significantly different trophic niche from all other fish. Many rivers in central Mexico share similar anthropogenic impacts and similar biotas, such that food web patterns described here are likely indicative of other river systems in central Mexico. Copyright © 2008 John Wiley & Sons, Ltd.
@article{Mercado-Silva2008, author = {Mercado-Silva, Norman and Helmus, Matthew R. and Vander Zanden, M. Jake }, title = {The effects of impoundment and non-native species on a river food web in Mexico's central plateau}, journal = {River Research and Applications}, year = {2008}, }
|Paoli, Gary and Curran, Lisa and Slik, J.
|Soil nutrients affect spatial patterns of aboveground biomass and emergent tree density in southwestern Borneo
Vol. 155, pp. 287--299
|Abstract:Abstract Studies on the relationship between soil fertility and aboveground biomass in lowland tropical forests have yielded conflicting results, reporting positive, negative and no effect of soil nutrients on aboveground biomass. Here, we quantify the impact of soil variation on the stand structure of mature Bornean forest throughout a lowland watershed (8?196 m a.s.l.) with uniform climate and heterogeneous soils. Categorical and bivariate methods were used to quantify the effects of (1) parent material differing in nutrient content (alluvium > sedimentary > granite) and (2) 27 soil parameters on tree density, size distribution, basal area and aboveground biomass. Trees ?10 cm (diameter at breast height, dbh) were enumerated in 30 (0.16 ha) plots (sample area = 4.8 ha). Six soil samples (0?20 cm) per plot were analyzed for physiochemical properties. Aboveground biomass was estimated using allometric equations. Across all plots, stem density averaged 521 ñ 13 stems ha?1, basal area 39.6 ñ 1.4 m2 ha?1 and aboveground biomass 518 ñ 28 Mg ha?1 (mean ñ SE). Adjusted forest-wide aboveground biomass to account for apparent overestimation of large tree density (based on 69 0.3-ha transects; sample area = 20.7 ha) was 430 ñ 25 Mg ha?1. Stand structure did not vary significantly among substrates, but it did show a clear trend toward larger stature on nutrient-rich alluvium, with a higher density and larger maximum size of emergent trees. Across all plots, surface soil phosphorus (P), potassium, magnesium and percentage sand content were significantly related to stem density and/or aboveground biomass (R Pearson = 0.368?0.416). In multiple linear regression, extractable P and percentage sand combined explained 31% of the aboveground biomass variance. Regression analyses on size classes showed that the abundance of emergent trees >120 cm dbh was positively related to soil P and exchangeable bases, whereas trees 60?90 cm dbh were negatively related to these factors. Soil fertility thus had a significant effect on both total aboveground biomass and its distribution among size classes.
@article{Paoli2008, author = {Paoli, Gary and Curran, Lisa and Slik, J.}, title = {Soil nutrients affect spatial patterns of aboveground biomass and emergent tree density in southwestern Borneo}, journal = {Oecologia}, year = {2008}, number = {2}, volume = {155}, pages = {287--299}, url = {http://dx.doi.org/10.1007/s00442-007-0906-9} }
|Slik, J. and Bernard, Caroline and Van Beek, Marloes and Breman, Floris and Eichhorn, Karl A. O.
|Tree diversity, composition, forest structure and aboveground biomass dynamics after single and repeated fire in a Bornean rain forest
Vol. 158, pp. 579-588
|Abstract:Abstract Forest fires remain a devastating phenomenon in the tropics that not only affect forest structure and biodiversity, but also contribute significantly to atmospheric CO2. Fire used to be extremely rare in tropical forests, leaving ample time for forests to regenerate to pre-fire conditions. In recent decades, however, tropical forest fires occur more frequently and at larger spatial scales than they used to. We studied forest structure, tree species diversity, tree species composition, and aboveground biomass during the first 7 years since fire in unburned, once burned and twice burned forest of eastern Borneo to determine the rate of recovery of these forests. We paid special attention to changes in the tree species composition during burned forest regeneration because we expect the long-term recovery of aboveground biomass and ecosystem functions in burned forests to largely depend on the successful regeneration of the pre-fire, heavy-wood, species composition. We found that forest structure (canopy openness, leaf area index, herb cover, and stem density) is strongly affected by fire but shows quick recovery. However, species composition shows no or limited recovery and aboveground biomass, which is greatly reduced by fire, continues to be low or decline up to 7 years after fire. Consequently, large amounts of the C released to the atmosphere by fire will not be recaptured by the burned forest ecosystem in the near future. We also observed that repeated fire, with an inter-fire interval of 15 years, does not necessarily lead to a huge deterioration in the regeneration potential of tropical forest. We conclude that burned forests are valuable and should be conserved and that long-term monitoring programs in secondary forests are necessary to determine their recovery rates, especially in relation to aboveground biomass accumulation.
@article{Slika, author = {Slik, J. and Bernard, Caroline and Van Beek, Marloes and Breman, Floris and Eichhorn, Karl A. O.}, title = {Tree diversity, composition, forest structure and aboveground biomass dynamics after single and repeated fire in a Bornean rain forest}, journal = {Oecologia}, year = {2008}, number = {3}, volume = {158}, pages = {579-588}, url = {http://dx.doi.org/10.1007/s00442-008-1163-2} }
|Slik, J. W. Ferry and Bernard, Caroline S. and Bremen, Floreis C. and Beek, Maroles Van and Salim, Agus and Sheil, Douglas
|Wood Density as a Conservation Tool: Quantification of Disturbance and Identification of Conservation-Priority Areas in Tropical Forests
|Conservation Biology
Vol. 22, pp. 1299--1308
|Abstract:Inventories of tree species are often conducted to guide conservation efforts in tropical forests. Such surveys are time consuming, demanding of expertise, and expensive to perform and interpret. Approaches to make survey efforts simpler or more effective would be valuable. In particular, it would be good to be able to easily identify areas of old-growth forest. The average density of the wood of a tree species is closely linked to its successional status. We used tree inventory data from eastern Borneo to determine whether wood density can be used to quantify forest disturbance and conservation importance. The average density of wood in a plot was significantly and negatively related to disturbance levels, with plots with higher wood densities occurring almost exclusively in old-growth forests. Average wood density was unimodally related to the diversity of tree species, indicating that the average wood density in a plot might be a better indicator of old-growth forest than species diversity. In addition, Borneo endemics had significantly heavier wood than species that are common throughout the Malesian region, and they were more common in plots with higher average wood density. We concluded that wood density at the plot level could be a powerful tool for identifying areas of conservation priority in the tropical rain forests of Southeast Asia. Los inventarios de ?rboles a menudo son llevados a cabo para guiar los esfuerzos de conservaci?n en bosques tropicales. Tales inventarios consumen tiempo, demandan profesionalismo y su realizaci?n e interpretaci?n son costosas. M?todos para que los esfuerzos fueran m?s simples o m?s efectivos ser?an muy valiosos. En particular, ser?a bueno poder identificar ?reas de bosque maduro f?cilmente. La densidad promedio de madera de una especie de ?rbol se relaciona estrechamente con el estatus sucesional. Utilizamos datos del inventario de ?rboles de Borneo oriental y de densidad de madera para determinar s? la densidad de la madera se puede utilizar para cuantificar la perturbaci?n del bosque y su importancia para la conservaci?n. La densidad promedio de madera en una parcela se relacion? significativa y negativamente con los niveles de perturbaci?n, las parcelas con las mayores densidades de madera ocurrieron casi exclusivamente en los bosques maduros. La densidad promedio de madera se relacion? unimodalmente con la diversidad de especies de ?rboles, lo que indica que la densidad promedio de madera en una parcela puede ser un mejor indicador de un bosque maduro que la diversidad de especies. Adicionalmente, las especies end?micas de Borneo ten?an madera significativamente m?s pesada que las especies que son comunes en la reg?on Malesiana, y fueron m?s comunes en parcelas con mayor densidad promedio de madera. Concluimos que la densidad de madera a nivel de parcela pudiera ser una herramienta poderosa para la identificaci?n de ?reas de prioridad para la conservaci?n en los bosques tropicales lluviosos del sureste de Asia.
@article{SLIK2008, author = {Slik, J. W. Ferry and Bernard, Caroline S. and Bremen, Floreis C. and Beek, Maroles Van and Salim, Agus and Sheil, Douglas}, title = {Wood Density as a Conservation Tool: Quantification of Disturbance and Identification of Conservation-Priority Areas in Tropical Forests}, journal = {Conservation Biology}, year = {2008}, number = {5}, volume = {22}, pages = {1299--1308}, url = {http://dx.doi.org/10.1111/j.1523-1739.2008.00986.x} }
|Webb, C. O and Cannon, C. H and Davies, S. J
|Ecological organization, biogeography, and the phylogenetic structure of tropical forest tree communities
|Tropical Forest Community Ecology
|Book Part
@incollection{Webb2008, author = {Webb, C. O and Cannon, C. H and Davies, S. J}, title = {Ecological organization, biogeography, and the phylogenetic structure of tropical forest tree communities}, journal = {Tropical Forest Community Ecology}, year = {2008}, pages = {--}, }
|Cannon, C. H and Curran, L. M and Marshall, A. J and Leighton, M.
|Beyond mastfruiting events: community asynchrony and individual dormancy dominate woody plant reproductive behavior across seven Bornean forest types.
|Current Science
Vol. 93, pp. 21-29
@article{Cannon2007c, author = {Cannon, C. H and Curran, L. M and Marshall, A. J and Leighton, M.}, title = {Beyond mastfruiting events: community asynchrony and individual dormancy dominate woody plant reproductive behavior across seven Bornean forest types.}, journal = {Current Science}, year = {2007}, number = {11}, volume = {93}, pages = {21-29}, }
|Cannon, C. H and Curran, L. M and Marshall, A. J and Leighton, M.
|Long-term reproductive behavior of woody plants across seven Bornean forest types in the Gunung Palung National Park (Indonesia): suprannual synchrony, temporal productivity, and fruiting diversity
|Ecology Letters
Vol. 10, pp. 956--969
@article{Cannon2007a, author = {Cannon, C. H and Curran, L. M and Marshall, A. J and Leighton, M.}, title = {Long-term reproductive behavior of woody plants across seven Bornean forest types in the Gunung Palung National Park (Indonesia): suprannual synchrony, temporal productivity, and fruiting diversity}, journal = {Ecology Letters}, year = {2007}, number = {10}, volume = {10}, pages = {956--969}, }
|Cannon, C. H. and Summers, M. and Harting, J.R. and Keßler, P.J.A.
|Developing conservation priorities based on forest type, condition, and threats in a poorly known ecoregion: Sulawesi, Indonesia
Vol. 39, pp. 747--759
@article{Cannon2007, author = {Cannon, C. H. and Summers, M. and Harting, J.R. and Keßler, P.J.A.}, title = {Developing conservation priorities based on forest type, condition, and threats in a poorly known ecoregion: Sulawesi, Indonesia}, journal = {Biotropica}, year = {2007}, number = {6}, volume = {39}, pages = {747--759}, }
|Helmus, Matthew R. and Bland, Thomas J. and Williams, Christopher K. and Ives, Anthony R.
|Phylogenetic Measures of Biodiversity
|The American Naturalist
Vol. 169, pp. E68-E83
|Abstract:We developed a theoretical framework based on phylogenetic comparative methods to integrate phylogeny into three measures of biodiversity: species variability, richness, and evenness. These metrics can be used in conjunction with permutation procedures to test for phylogenetic community structure. As an illustration, we analyzed data on the composition of 58 lake fish communities in Wisconsin. The fish communities showed phylogenetic underdispersion, with communities more likely to contain closely related species. Using information about differences in environmental characteristics among lakes, we demonstrated that phylogenetic underdispersion in fish communities was associated with environmental factors. For example, lakes with low pH were more likely to contain species in the same clade of acid‐tolerant species. Our metrics differ from existing metrics used to calculate phylogenetic community structure, such as net relatedness index and Faith's phylogenetic diversity. Our metrics have the advantage of providing an integrated and easy‐to‐understand package of phylogenetic measures of species variability, richness, and evenness with well‐defined statistical properties. Furthermore, they allow the easy evaluation of contributions of individual species to different aspects of the phylogenetic organization of communities. Therefore, these metrics should aid with the incorporation of phylogenetic information into strategies for understanding biodiversity and its conservation.
@electronic{Matthew2007, author = {Helmus, Matthew R. and Bland, Thomas J. and Williams, Christopher K. and Ives, Anthony R.}, title = {Phylogenetic Measures of Biodiversity}, journal = {The American Naturalist}, year = {2007}, number = {3}, volume = {169}, pages = {E68-E83}, }
|Helmus, Matthew R. and Savage, Kristina and Diebel, Matthew W. and Maxted, Jeffrey T. and Ives, Anthony R.
|Separating the determinants of phylogenetic community structure
|Ecology Letters
Vol. 10, pp. 917-925
|Abstract:The role of competition in forbidding similar species from co-occurring has long been debated. A difficulty in identifying this repulsion of similar species is that similar species share similar environmental requirements and hence show an attraction to communities where these requirements are met. To disentangle these opposing patterns, we use phylogenetic relatedness as an objective metric of species similarities. Studying 11 sunfishes (Centrarchidae) from 890 lakes, we first show no phylogenetic pattern in the raw community data. We then regressed sunfish presence/absence against seven environmental variables and show that lakes with similar water clarity and latitude likely contain closely related species. After statistically removing the environmental effects, phylogenetic repulsion was apparent, with closely related sunfishes less likely to co-occur. Thus, both phylogenetic attraction, driven by environmental filtering, and phylogenetic repulsion, possibly caused by competition, simultaneously occur and obscure one another in the overall phylogenetic structure of sunfish communities.
@article{Helmus2007, author = {Helmus, Matthew R. and Savage, Kristina and Diebel, Matthew W. and Maxted, Jeffrey T. and Ives, Anthony R. }, title = {Separating the determinants of phylogenetic community structure}, journal = {Ecology Letters}, year = {2007}, number = {10}, volume = {10}, pages = {917-925}, }
|Newton, Ryan J. and Jones, Stuart E. and Helmus, Matthew R. and McMahon, Katherine D.
|Phylogenetic Ecology of the Freshwater Actinobacteria acI Lineage
|Applied and Environmental Microbiology
Vol. 73, pp. 7169--7176
|Abstract:The acI lineage of freshwater Actinobacteria is a cosmopolitan and often numerically dominant member of lake bacterial communities. We conducted a survey of acI 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions from 18 Wisconsin lakes and used standard nonphylogenetic and phylogenetic statistical approaches to investigate the factors that determine acI community composition at the local scale (within lakes) and at the regional scale (across lakes). Phylogenetic reconstruction of 434 acI 16S rRNA genes revealed a well-defined and highly resolved phylogeny. Eleven previously unrecognized monophyletic clades, each with ≥97.9% within-clade 16S rRNA gene sequence identity, were identified. Clade community similarity positively correlated with lake environmental similarity but not with geographic distance, implying that the lakes represent a single biotic region containing environmental filters for communities that have similar compositions. Phylogenetically disparate clades within the acI lineage were most abundant at the regional scale, and local communities were comprised of more closely related clades. Lake pH was a strong predictor of the community composition, but only when lakes with a pH below 6 were included in the data set. In the remaining lakes (pH above 6) biogeographic patterns in the landscape were instead a predictor of the observed acI community structure. The nonrandom distribution of the newly defined acI clades suggests potential ecophysiological differences between the clades, with acI clades AI, BII, and BIII preferring acidic lakes and acI clades AII, AVI, and BI preferring more alkaline lakes.
@article{Newton2007, author = {Newton, Ryan J. and Jones, Stuart E. and Helmus, Matthew R. and McMahon, Katherine D.}, title = {Phylogenetic Ecology of the Freshwater Actinobacteria acI Lineage}, journal = {Applied and Environmental Microbiology}, year = {2007}, number = {22}, volume = {73}, pages = {7169--7176}, }
|Cannon, C. H and Kua, C. S and Lobenhofer, E. K and Hurban, P.
|Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform
|Nucleic Acids Research
Vol. 34, pp. Art. No. e121--Art. No. e121
@article{Cannon2006, author = {Cannon, C. H and Kua, C. S and Lobenhofer, E. K and Hurban, P.}, title = {Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform}, journal = {Nucleic Acids Research}, year = {2006}, number = {18}, volume = {34}, pages = {Art. No. e121--Art. No. e121}, }
|Slik, J. and Van Balen, S.
|Bird Community Changes in Response to Single and Repeated Fires in a Lowland Tropical Rainforest of Eastern Borneo
|Biodiversity and Conservation
Vol. 15, pp. 4425--4451
|Abstract:Abstract Our current understanding of bird community responses to tropical forest fires is limited and strongly geographically biased towards South America. Here we used the circular plot method to carry out complete bird inventories in undisturbed, once burned (1998) and twice burned forests (1983 and 1998) in East Kalimantan (Indonesia). Additionally, environmental variables were measured within a 25 m radius of each plot. Three years after fire the number of birds and bird species were similar for undisturbed and burned forests, but species diversity and turnover were significantly lower in the burned forests. The bird species composition also differed significantly between undisturbed and burned forests, with a strong decline of closed forest preferring bird species accompanied by a strong increase in degraded forest preferring species in burned forests. These differences were strongly related to differences in environmental conditions such as shifts in vegetation cover and layering and differences in ground and understorey vegetation structure. We also found significant shifts in body mass distribution, foraging height and feeding guilds between the bird communities in unburned and burned forests. Surprisingly, repeated burning did not lead to increasing impoverishment of the avifauna, and both once and twice burned forests still contained most of the bird species that were also present in undisturbed forest, even though their densities were considerably lowered.
@article{Slik2006, author = {Slik, J. and Van Balen, S.}, title = {Bird Community Changes in Response to Single and Repeated Fires in a Lowland Tropical Rainforest of Eastern Borneo}, journal = {Biodiversity and Conservation}, year = {2006}, number = {14}, volume = {15}, pages = {4425--4451}, url = {http://dx.doi.org/10.1007/s10531-005-4385-1} }
|Slik, JWF
|Estimating species-specific wood density from the genus average in Indonesian trees
|Journal of Tropical Ecology
Vol. 22, pp. 481--482
@article{Slik2006a, author = {Slik, JWF}, title = {Estimating species-specific wood density from the genus average in Indonesian trees}, journal = {Journal of Tropical Ecology}, year = {2006}, volume = {22}, pages = {481--482}, url = {http://dx.doi.org/10.1017/S0266467406003324} }
|Zhang, B. H and Pan, X. P and Cannon, C. H and Cobb, G. P and Anderson, T. A
|Conservation and divergence of plant microRNA genes
|Plant Journal
Vol. 46, pp. 243--259
@article{Zhang2006, author = {Zhang, B. H and Pan, X. P and Cannon, C. H and Cobb, G. P and Anderson, T. A}, title = {Conservation and divergence of plant microRNA genes}, journal = {Plant Journal}, year = {2006}, number = {2}, volume = {46}, pages = {243--259}, }
|Asif, M. J and Cannon, C. H
|DNA extraction from processed wood: A case study for the identi?cation of an endangered timber species (Gonystylus bancanus)
|Plant Molecular Biology Reporter
Vol. 23, pp. 185--192
|Abstract:We applied human forensic techniques to the extraction of whole genomic DNA from processed wood samples to explore the possibility of identifying an endangered tropical timber species by using DNA sequencing technology. High-yield and high-quality DNA samples were obtained from 2 commercial wood and 3 herbarium samples. Large PCR fragments ranging from 500-800 bp were successfully ampli?ed from 2 chloroplast and I mitochondrial regions in all 5 samples, indicating limited degradation of the cytoplasmic genomes. DNA extraction from stem wood taken from herbarium specimens appeared superior to that from stem wood with bark intact or from leaf samples. DNA sequences from the trn regions allowed for easy identi?cation of the focal species based on GenBank Blast search. Little sequence variation was observed in the 3 regions, with the mitochondrial cox3 region completely conserved. Extraction of high-quality and large intact DNA fragments makes dry wood materials amenable to various DNA marker-based applications, including ?ngerprinting and historical approaches. By sampling stemwood, the wealth of historical information housed in international herbaria can be explored with minimal damage to taxonomically important features.
@article{Asif2005, author = {Asif, M. J and Cannon, C. H}, title = {DNA extraction from processed wood: A case study for the identi?cation of an endangered timber species (Gonystylus bancanus)}, journal = {Plant Molecular Biology Reporter}, year = {2005}, number = {2}, volume = {23}, pages = {185--192}, }
|Cannon, C. H and Harting, J. R and S., Agus and Summers, M.
|The vegetation of Sulawesi: II. fine filter analysis
@techreport{Cannon2005a, author = {Cannon, C. H and Harting, J. R and S., Agus and Summers, M.}, title = {The vegetation of Sulawesi: II. fine filter analysis}, year = {2005}, pages = {--}, }
|Cannon, C. H and Harting, J. R and Salim, A. and Summers, M.
|Vegetation of Sulawesi: I. coarse filter analysis
@techreport{Cannon2005, author = {Cannon, C. H and Harting, J. R and Salim, A. and Summers, M.}, title = {Vegetation of Sulawesi: I. coarse filter analysis}, year = {2005}, pages = {--}, }
|Harting, J. R and Cannon, C. H
|The vegetation of Sulawesi: forest change analysis
@techreport{Harting2005, author = {Harting, J. R and Cannon, C. H}, title = {The vegetation of Sulawesi: forest change analysis}, year = {2005}, pages = {--}, }
|Helmus, Matthew R. and Dussourd, David E.
|Glues or poisons: which triggers vein cutting by monarch caterpillars?
Vol. 15, pp. 45-49
|Abstract:Late instar larvae of the monarch butterfly (Danaus plexippus L., Lepidoptera: Nymphalidae) deactivate the latex defense of milkweeds by chewing a furrow in the leaf midrib or petiole. The larva then feeds beyond the cut where latex outflow is minimal. If a larva does encounter latex exudate during feeding, it often returns to its initial cut to damage the midrib or petiole more extensively before resuming feeding. We used this response to latex as an assay for testing what cue triggers vein cutting. A sticky solution of polyethylene glycol and a mixture of cardenolides both were ineffective; drops applied to the mouthparts of feeding monarchs failed to elicit renewed vein cutting. Activity resided instead within a methanol extract of the supernatant obtained from centrifuged latex of the milkweed, Asclepias curassavica L. (Asclepiadaceae). Treatment with proteinase K did not eliminate activity documenting that the active compound is unlikely to be proteinaceous. Our results indicate that latex adhesiveness and low polarity cardenolides are relatively unimportant releasers of vein cutting. We propose that milkweeds contain noncardenolide stimulants of vein cutting; these compounds presumably serve a defensive role for milkweeds. Over 50 species of insects are known to employ vein-cutting before feeding on plants with canal-borne exudates; most of these species are dietary specialists like the monarch. Our behavioral assay provides a novel approach for identifying ecologically-significant compounds in the exudates of their diverse host plants.
@article{Helmus2005, author = {Helmus, Matthew R. and Dussourd, David E. }, title = {Glues or poisons: which triggers vein cutting by monarch caterpillars?}, journal = {Chemoecology}, year = {2005}, number = {1}, volume = {15}, pages = {45-49}, }
|Sierra, S. E. C. and Welzen, P. C. and Slik, J. W. F.
|A taxonomic revision of Mallotus section Philippinenses (former section Rottlera-Euphorbiaceae) in Malesia and Thailand.
Vol. 50, pp. 221--248
|Abstract:Aim To (1) identify floristic regions in the lowland (below 500 m a.s.l.) tropical dipterocarp rain forest of Borneo based on tree genera, (2) determine the characteristic taxa of these regions, (3) study tree diversity patterns within Borneo, and (4) relate the floristic and diversity patterns to abiotic factors such as mean annual rainfall and geographical distance between plots.
@article{Sierra2005, author = {Sierra, S. E. C. and Welzen, P. C. and Slik, J. W. F.}, title = {A taxonomic revision of Mallotus section Philippinenses (former section Rottlera-Euphorbiaceae) in Malesia and Thailand.}, journal = {Blumea}, year = {2005}, number = {2}, volume = {50}, pages = {221--248}, url = {http://openurl.ingenta.com/content?genre=article&issn=0006-5196&volume=50&issue=2&spage=221&epage=248} }
|Slik, JWF
|Assessing tropical lowland forest disturbance using plant morphological and ecological attributes
Vol. 205, pp. 241--250
|Abstract:Secondary forests now play a vital role in the conservation of tree species diversity in Southeast Asia because of the continuing fragmentation and decreasing extent of undisturbed forests in this region. To be able to determine the structural and compositional integrity of secondary forests, a ground based rapid assessment method was developed. For this purpose species from the genera Macaranga and Mallotus (Euphorbiaccae) were classified into early and late successional species based on morphological characters that were found to correlate with the light establishment preferences of these species. These characters were wood density (found to be significantly negatively correlated with light establishment preference), seed size (also significantly negatively correlated with light establishment preference), and leaf shape (the leaf length/width ratio was significantly negatively correlated with light establishment preference). Based on this species classification, number of pioneers and non-pioneers could be determined in 71 plots of 0.3 ha. covering 11 common forest disturbance types in Southeast Asia. Three main patterns were detected with this methodology: (1) pioneer and non-pioneer densities were significantly correlated with the forest disturbance level: (2) pioneer densities decreased with time since disturbance; (3) pioneer densities increased with repeated disturbance. A sample size test indicated that forest disturbance in general, and the differences between the major disturbance types could be significantly determined with a minimum of five plots of 0.3 ha. (C) 2004 Elsevier B.V. All rights reserved.
@article{Slik2005, author = {Slik, JWF}, title = {Assessing tropical lowland forest disturbance using plant morphological and ecological attributes}, journal = {FOREST ECOLOGY AND MANAGEMENT}, year = {2005}, number = {1-3}, volume = {205}, pages = {241--250}, url = {http://dx.doi.org/10.1016/j.foreco.2004.10.011} }
|Cannon, C. H. and Leighton, M.
|Tree species distributions across five habitats in a Bornean rain forest
|Journal of Vegetation Science
Vol. 15, pp. 257--266
|Abstract:We examined the distribution of tree species across five habitats in 69 small plots within a single watershed of the Gunung Palung National Park, West Kalimantan, Indonesia (GPNP). The spatially complex distribution and close proximity of habitats provided an opportunity to test habitat specificity of tree species across strong environmental gradients, in a situation where dispersal into 'inappropriate' habitat should not be a rare event. Habitat had a weak influence on community structure, although species diversity was lower in the alluvium and peat habitats. Association tests based on two randomization models (spatially independent and explicit) were used to examine habitat distribution of 55 'common' and 142 'frequent' taxa. The general patterns were similar in the two models but the interpretation of specific patterns depended greatly on assumptions about dispersal ability. A majority (67%) of the common species was significantly associated with a single habitat, while few were restricted to one habitat. A small proportion (16%) of the species appear to be habitat generalists. The peat habitat had the most profound effect on species distribution. Overall, a large amount of variation was found in the degree of habitat specificity, even within speciose groups. No obvious evolutionary or ecological correlates with degree of habitat specificity were found. These results suggest that a mixture of stochastic and deterministic processes determine species distribution even across strong environmental gradients.
@article{Cannon2004, author = {Cannon, C. H. and Leighton, M.}, title = {Tree species distributions across five habitats in a Bornean rain forest}, journal = {Journal of Vegetation Science}, year = {2004}, number = {2}, volume = {15}, pages = {257--266}, }
|Slik, J. W. F.
|El Niño droughts and their effects on tree species composition and diversity in tropical rain forests
Vol. 141, pp. 114--120
|Abstract:In this study I investigated the effects of the extreme, 1997/98 El Niño related drought on tree mortality and understorey light conditions of logged and unlogged tropical rain forest in the Indonesian province of East Kalimantan (Borneo). My objectives were to test (1) whether drought had a significant effect on tree mortality and understorey light conditions, (2) whether this effect was greater in logged than in undisturbed forest, (3) if the expected change in tree mortality and light conditions had an effect on Macaranga pioneer seedling and sapling densities, and (4) which (a)biotic factors influenced tree mortality during the drought. The 1997/1998 drought led to an additional tree mortality of 11.2, 18.1, and 22.7% in undisturbed, old logged and recently logged forest, respectively. Mortality was highest in logged forests, due to extremely high mortality of pioneer Macaranga trees (65.4%). Canopy openness was significantly higher during the drought than during the non-drought year (6.0, 8.6 and 10.4 vs 3.7, 3.8 and 3.7 in undisturbed, old logged and recently logged forest, respectively) and was positively correlated with the number of dead standing trees. The increase in light in the understorey was accompanied by a 30 to 300-fold increase in pioneer Macaranga seedling densities. Factors affecting tree mortality during drought were (1) tree species successional status, (2) tree size, and (3) tree location with respect to soil moisture. Tree density and basal area per surface unit had no influence on tree mortality during drought. The results of this study show that extreme droughts, such as those associated with El Niño events, can affect the tree species composition and diversity of tropical forests in two ways: (1) by disproportionate mortality of certain tree species groups and tree size classes, and (2) by changing the light environment in the forest understorey, thereby affecting the recruitment and growth conditions of small and immature trees.
@article{Slik2004, author = {Slik, J. W. F.}, title = {El Niño droughts and their effects on tree species composition and diversity in tropical rain forests}, journal = {Oecologia}, year = {2004}, number = {1}, volume = {141}, pages = {114--120}, url = {http://dx.doi.org/10.1007/s00442-004-1635-y} }
|Cannon, C. H. and Manos, P. S.
|Phylogeography of the Southeast Asian stone oaks (Lithocarpus)
|Journal of Biogeography
Vol. 30, pp. 211--226
@article{Cannon2003, author = {Cannon, C. H. and Manos, P. S.}, title = {Phylogeography of the Southeast Asian stone oaks (Lithocarpus)}, journal = {Journal of Biogeography}, year = {2003}, volume = {30}, pages = {211--226}, }
|Slik, Ferry J. W. and Keßler, Paul J. A. and van Welzen, Peter C.
|Macaranga and Mallotus species (Euphorbiaceae) as indicators for disturbance in the mixed lowland dipterocarp forest of East Kalimantan (Indonesia)
|Ecological Indicators
Vol. 2, pp. 311--324
|Abstract:The indicator value (IV) of Macaranga and Mallotus species (Euphorbiaceae) for di?erent types of disturbance in lowland dipterocarp forest was assessed by counting and identifying all individuals of species of these genera taller than 30 cm in 45 (10 x 300 m) plots at nine locations. Twelve Macaranga and nine Mallotus species were found. The main forest disturbance types (primary forest, secondary forest, selectively logged forest, forest burned once, and repeatedly burned forest used for shifting cultivation) each had their own set of indicator species. The level of disturbance in the forest types was assessed by measuring nine forest structural parameters. The occurrence of Macaranga and Mallotus species was closely related to the level of disturbance in a forest. Most Macaranga species were characteristic of high disturbance levels, while most Mallotus species preferred intermediate to low levels of disturbance. However, both genera had species at both disturbance extremes. Using multiple regression analysis, combinations of Macaranga and Mallotus species were formed and used to predict the separate forest structural parameters and the general level of disturbance of a forest. The Macaranga and Mallotus species could be grouped into (1) primary forest 'remnant' species; (2) generalist pioneer species; and (3) high disturbance pioneer species.
@article{FerrySlik2003, author = {Slik, Ferry J. W. and Keßler, Paul J. A. and van Welzen, Peter C.}, title = {Macaranga and Mallotus species (Euphorbiaceae) as indicators for disturbance in the mixed lowland dipterocarp forest of East Kalimantan (Indonesia)}, journal = {Ecological Indicators}, year = {2003}, number = {4}, volume = {2}, pages = {311--324}, url = {http://www.sciencedirect.com/science/article/B6W87-487KF92-1/2/422687781d62c44bf708d3357798f8c4} }
|Slik, J. W. F. and Poulsen, A. D. and Ashton, P. S. and Cannon, C. H. and Eichhorn, K. A. O. and Kartawinata, K. and Lanniari, I. and Nagamasu, H. and Nakagawa, M. and van Nieuwstadt, M. G. L.
|A floristic analysis of the lowland dipterocarp forests of Borneo
|Journal of Biogeography
Vol. 30, pp. 1517--1531
|Abstract:Aim To (1) identify floristic regions in the lowland (below 500 m asl) tropical dipterocarp rain forest of Borneo based on tree species, (2) determine the characteristic taxa of these regions, (3) study tree diversity patterns within Borneo, and (4) relate the floristic and diversity patterns to abiotic factors such as mean annual rainfall and geographic distance between plots. Location Lowland tropical dipterocarp rain forest of Borneo. Methods We used tree (diameter at breast height 9.8 cm) inventory data from 28 lowland dipterocarp rain forest locations throughout Borneo. From each location 6 samples of 640 individuals were drawn randomly. With these data we calculated a Sørensen and Steinhaus similarity matrix for the locations. These matrices were then used in an UPGMA clustering algorithm to determine the floristic relations between the locations (dendrogram). Principal Coordinate analysis was used to ordinate the locations. Characteristic taxa for the identified floristic clusters were determined with the use of the INDVAL method of Dufrene &Legendre (1997). Finally, Mantel analysis was applied to determine the influence of mean annual rainfall and geographic distance between plots on floristic composition. Results A total of 77 families and 363 genera were included in the analysis. On average a random sample of 640 trees from a lowland dipterocarp forest in Borneo contains 41.6 ± 3.8 families and 103.0 ± 12.7 genera. Diversity varied strongly on local scales. On a regional scale, diversity was found to be highest in southeast Borneo and central Sarawak. The most common families were Dipterocarpaceae (21.9% of trees) and Euphorbiaceae (12.2% of trees). The most common genera were Shorea (12.3% of trees) and Syzygium (5.0% of trees). The 28 locations were clustered in geographically distinct floristic regions. This was related to the fact that floristic similarity depended strongly on the geographic distance between plots and similarity in mean annual rainfall. Conclusions We identified five main floristic regions within the lowland dipterocarp rain forests of Borneo, each of which had its own set of characteristic genera. Mean annual rainfall is an important factor in explaining differences in floristic composition between locations. The influence of geographic distance on floristic similarity between locations is probably related to the fact that abiotic factors change with distance between plots. Borneo's central mountain range generally forms an effective dispersal barrier for the lowland tree flora. Diversity patterns in Borneo are influenced by the mid domain effect, habitat size, and the influence of past climatic changes (ice ages during the Pleistocene).
@article{Slik2003, author = {Slik, J. W. F. and Poulsen, A. D. and Ashton, P. S. and Cannon, C. H. and Eichhorn, K. A. O. and Kartawinata, K. and Lanniari, I. and Nagamasu, H. and Nakagawa, M. and van Nieuwstadt, M. G. L.}, title = {A floristic analysis of the lowland dipterocarp forests of Borneo}, journal = {Journal of Biogeography}, year = {2003}, number = {10}, volume = {30}, pages = {1517--1531}, url = {http://dx.doi.org/10.1046/j.1365-2699.2003.00967.x} }
|Slik, J.W.F. and Eichhorn, K.A.O.
|Fire survival of lowland tropical rain forest trees in relation to stem diameter and topographic position
Vol. 137, pp. 446--455
|Abstract:The objective of this study was to relate patterns in forest structure, tree species diversity, and tree species composition to stem diameters and topography in unburned, once burned and twice burned lowland dipterocarp rain forests in East Kalimantan, Indonesia. To do this four unburned old growth forests were compared with three forests that burned once (1997/1998) and three forests that burned twice (1982/1983 and 1997/1998). Fire resulted in a strong reduction of climax tree density which was negatively related to tree diameter. However, a disproportionate reduction in small diameter understorey climax tree species occurred only after repeated fires. Climax tree species in both burned forest types were most common in swamps, river valleys and on lower slopes, while their density was much lower on places higher along hillsides. In unburned forest the opposite was observed, with climax tree density increasing steadily from swamp and river valleys to upper slopes and ridges. In contrast to climax trees, pioneer trees were abundant throughout the burned forest, with highest numbers on hill sides and ridges. Our results indicate that both diameter and topographic position of trees strongly affect their fire survival chances in tropical lowland forests.
@article{Slik2003b, author = {Slik, J.W.F. and Eichhorn, K.A.O.}, title = {Fire survival of lowland tropical rain forest trees in relation to stem diameter and topographic position}, journal = {Oecologia}, year = {2003}, number = {3}, volume = {137}, pages = {446--455}, url = {http://dx.doi.org/10.1007/s00442-003-1359-4} }
|Slik, J.W. Ferry and Verburg, Rene W. and Keßler, Paul J.A
|Effects of fire and selective logging on the tree species composition of lowland dipterocarp forest in East Kalimantan, Indonesia
|Biodiversity and Conservation
Vol. 11, pp. 85--98
|Abstract:Tree species composition (diameter at breast height (dbh) = 10 cm) was studied in primary, selectively logged and heavily burnt forests in East Kalimantan, Indonesia. The number of trees, tree species, and the Fishers's-a diversity index were determined for the first 15 years (burnt forest) and 25 years (selectively logged forest) after disturbance. Additionally the population structure of six common and typical Macaranga pioneer tree species was compared through time between selectively logged, burnt and primary forest. Both selectively logged and burnt forest showed a significant reduction in number of trees and tree species per surface area directly after disturbance. Fire especially affected dominant tree species, while for selective logging the opposite was observed. In selectively logged forest the number of trees, tree species and the Fishers's-a index reached pre-disturbance levels within c. 15 years. For burnt forest, only the number of trees recovered to pre-disturbance levels. The number of tree species stayed constant after disturbance, while the Fishers's-a index decreased. The six studied Macaranga pioneer tree species seedlings were present in all forest types. Their density seems to be unrelated to light levels in the forest understorey but strongly related to the number of mature parent trees. Their sapling densities were strongly related to light levels in the forest understorey. The studied Macaranga species formed an important part of both under- and over-storey in burnt forest 15 years after disturbance, while they were almost absent in the understorey and only moderately common in the overstorey of selectively logged forest.
@article{FerrySlik2002, author = {Slik, J.W. Ferry and Verburg, Rene W. and Keßler, Paul J.A}, title = {Effects of fire and selective logging on the tree species composition of lowland dipterocarp forest in East Kalimantan, Indonesia}, journal = {Biodiversity and Conservation}, year = {2002}, number = {1}, volume = {11}, pages = {85--98}, url = {http://dx.doi.org/10.1023/A:1014036129075} }
|Cannon, C. H
|Morphological and molecular diversity in Lithocarpus (Fagaceae) of Mount Kinabalu
|Sabah Parks Nature Journal
Vol. 4, pp. 45--69
@article{Cannon2001a, author = {Cannon, C. H}, title = {Morphological and molecular diversity in Lithocarpus (Fagaceae) of Mount Kinabalu}, journal = {Sabah Parks Nature Journal}, year = {2001}, volume = {4}, pages = {45--69}, }
|Cannon, C. H
|Vegetation of Lore Lindu National Park, Sulawesi Tengah
@techreport{Cannon2001b, author = {Cannon, C. H}, title = {Vegetation of Lore Lindu National Park, Sulawesi Tengah}, year = {2001}, pages = {--}, }
|Cannon, C. H and Manos, P. S
|Combining and comparing continuous morphometric descriptors with a molecular phylogeny: the case of fruit evolution in the Bornean Lithocarpus (Fagaceae)
|Systematic Biology
Vol. 50, pp. 1--21
@article{Cannon2001, author = {Cannon, C. H and Manos, P. S}, title = {Combining and comparing continuous morphometric descriptors with a molecular phylogeny: the case of fruit evolution in the Bornean Lithocarpus (Fagaceae)}, journal = {Systematic Biology}, year = {2001}, number = {6}, volume = {50}, pages = {1--21}, }
|Manos, P. S and Zhou, Z. K and Cannon, C. H
|Systematics of Fagaceae: Phylogenetic tests of reproductive trait evolution
|International Journal of Plant Sciences
Vol. 162, pp. 1361--1379
|Abstract:The family Fagaceae includes nine currently recognized genera and ca. 1000 species, making it one of the largest and most economically important groups within the order Fagales. In addition to wide variation in cupule and fruit morphology, polymorphism in pollination syndrome (wind vs. generalistic insect) also contributes to the uniqueness of the family. Phylogenetic relationships were examined using 179 accessions spanning the taxonomic breadth of the family, emphasizing tropical, subtropical, and relictual taxa. Nuclear ribosomal DNA sequences encoding the 5.8S rRNA gene and two ?anking internal transcribed spacers (ITS) were used to evaluate phylogenetic hypotheses based on previous morphological cladistic analysis and intuitive schemes. Parsimony analyses rooted with Fagus supported two clades within the family, Trigonobalanus sensu lato and a large clade comprising Quercus and the castaneoid genera (Castanea + Castanopsis, Chrysolepis, Lithocarpus). Three DNA sequence data sets, 179-taxon ITS, 60- taxon ITS, and a 14-taxon combined nuclear and chloroplast (matK), were used to test a priori hypotheses of reproductive character state evolution. We used Templeton's (1983) test to assess alternative scenarios of single and multiple origins of derived and seemingly irreversible traits such as wind pollination, hypogeal cotyledons, and ?ower cupules. On the basis of previous exemplar-based and current in-depth analyses of Fagaceae, we suggest that wind pollination evolved at least three times and hypogeal cotyledons once. Although we could not reject the hypothesis that the acorn fruit type of Quercus is derived from a dichasium cupule, combined analysis provided some evidence for a relationship of Quercus to Lithocarpus and Chrysolepis, taxa with dichasially arranged pistillate ?owers, where each ?ower is surrounded by cupular tissue. This indicates that a more broadly de?ned ?ower cupule, in which individual pistillate ?owers seated within a separate cupule, may have a single origin.
@article{Manos2001, author = {Manos, P. S and Zhou, Z. K and Cannon, C. H}, title = {Systematics of Fagaceae: Phylogenetic tests of reproductive trait evolution}, journal = {International Journal of Plant Sciences}, year = {2001}, number = {6}, volume = {162}, pages = {1361--1379}, }
|Slik, J. W. F and Welzen, P. C. van
|A phylogeny of Mallotus (Euphorbiaceae) based on morphology: indications for a pioneer origin of Macaranga
Vol. 26, pp. --786-796
|Abstract:A phylogenetic parsimony analysis based on 76 morphological characters of 43 Mallotus, 3 Macaranga, 1 Claoxylon, 1 Cleidion, 1 Sampantaea, and 1 Wetria species, resulted in 314 trees of length 602 (CI =0.600, RI = 0.685), which could be summarized in a well resolved consensus cladogram. This consensus cladogram indicates that the genus Mallotus is possibly polyphyletic and that sections Hancea and Oliganthae should probably be excluded from Mallotus. It is proposed to refer to Mallotus as either Mallotus sensu lato (with the sections Hancea and Oliganthae) or Mallotus sensu stricto (excluding the sections Hancea and Oliganthae). The genus Macaranga forms a monophyletic group within Mallotus s.s. The traditional section delimitations within Mallotus s.s. do not circumscribe monophyletic clades of species with the exception of section Polyadenii. It is suggested that sections Stylanthus, Rottlera, Mallotus, and the genus Macaranga should form one monophyletic clade. Sections Axenfeldia and Rottleropsis remain unresolved, but are probably closely related. The position of Macaranga within Mallotus suggests that Macaranga evolved from pioneer ancestors that lived in open, scrub-like vegetation. It is hypothesised that Macaranga originated relatively recently in South East Asia during the Oligocene or early Miocene (between 38 and 15 million years ago).
@book{Slik2001, author = {Slik, J. W. F and Welzen, P. C. van}, title = {A phylogeny of Mallotus (Euphorbiaceae) based on morphology: indications for a pioneer origin of Macaranga}, year = {2001}, volume = {26}, pages = {--786-796}, }
|Slik, J. W. F.
|Welzen PC van. 2001 A phylogeny of Mallotus (Euphorbiaceae) based on morphology: indications for a pioneer origin of Macaranga
|Syst. Bot
Vol. 26, pp. 786--796
@article{Slik2001c, author = {Slik, J. W. F.}, title = {Welzen PC van. 2001 A phylogeny of Mallotus (Euphorbiaceae) based on morphology: indications for a pioneer origin of Macaranga}, journal = {Syst. Bot}, year = {2001}, number = {4}, volume = {26}, pages = {786--796}, }
|Slik, J. W. F. and Baas, P. and Keßler, P. J. A. and van Welzen, P. C. and te Leiden Pays-Bas, R.
|Macaranga and Mallotus (Euphorbiaceae) as Indicators for Disturbance in the Lowland Dipterocarp Forests of East Kalimantan, Indonesia
|Publisher: Tropenbos International
@book{Slik2001b, author = {Slik, J. W. F. and Baas, P. and Keßler, P. J. A. and van Welzen, P. C. and te Leiden Pays-Bas, R.}, title = {Macaranga and Mallotus (Euphorbiaceae) as Indicators for Disturbance in the Lowland Dipterocarp Forests of East Kalimantan, Indonesia}, publisher = {Tropenbos International}, year = {2001}, pages = {--}, }
|Slik, J. W. F. and van Welzen, P. C.
|A taxonomic revision of Mallotus sections Hancea and Stylanthus (Euphorbiaceae)
Vol. 46, pp. 3--66
@article{Slik2001a, author = {Slik, J. W. F. and van Welzen, P. C.}, title = {A taxonomic revision of Mallotus sections Hancea and Stylanthus (Euphorbiaceae)}, journal = {Blumea}, year = {2001}, number = {1}, volume = {46}, pages = {3--66}, }
|Bollendorff, S. M. and van Welzen, P. C. and Slik, J. W. F.
|A taxonomic revision of Mallotus section Polyadenii (Euphorbiaceae)
Vol. 45, pp. 319--340
@article{Bollendorff2000, author = {Bollendorff, S. M. and van Welzen, P. C. and Slik, J. W. F.}, title = {A taxonomic revision of Mallotus section Polyadenii (Euphorbiaceae)}, journal = {Blumea}, year = {2000}, number = {2}, volume = {45}, pages = {319--340}, }
|Cannon, C. H
|Macroevolutionary and phylogeographic studies of Lithocarpus (Fagaceae): gene ?ow and fruit evolution in a tropical tree
@phdthesis{Cannon2000, author = {Cannon, C. H}, title = {Macroevolutionary and phylogeographic studies of Lithocarpus (Fagaceae): gene ?ow and fruit evolution in a tropical tree}, year = {2000}, pages = {--}, }
|Cannon, C. H. and Manos, P. S.
|The Bornean Lithocarpus Bl. section Synaedrys (Lindl.) Barnett (Fagaceae): its circumscription and description of a new species
|Botanical Journal of the Linnean Society
Vol. 133, pp. 343--357
|Abstract:The Bornean species of Lithocarpus Bl, section Synaedrys (Lindl.) Barnett (Fagaceae) are discussed in terms of their unifying characteristics, and keys to the species are provided. A novel morphological feature present in the genus, where the seed in the mature fruit is enclosed by a lignified and thickened receptacle, is illustrated. A new species, L. palungensis Cannon & Manos, is described. It can be distinguished from L. pulcher (King) Markgr. by its submontane distribution, prominent reflexed cupular spines, present at all stages, and broadly oblong leaves with scattered open fasciculate trichomes on the abaxial surface. Foliar trichome types present within the section are also described. Distinctiveness of fruit wall and receptacle shape, as described by two-dimensional elliptic Fourier transformation, is demonstrated by principal components analysis. (C) 2000 The Linnean Society of London.
@article{Cannon2000a, author = {Cannon, C. H. and Manos, P. S.}, title = {The Bornean Lithocarpus Bl. section Synaedrys (Lindl.) Barnett (Fagaceae): its circumscription and description of a new species}, journal = {Botanical Journal of the Linnean Society}, year = {2000}, number = {3}, volume = {133}, pages = {343--357}, }
|Slik, J. W. F. and Priyono, W.
|Key to the Macaranga and Mallotus species (Euphorbiaceae) of east Kalimantan (Indonesia)
|Gardens Bull. Singapore
Vol. 52, pp. 11?87--11?87
@article{Slik, author = {Slik, J. W. F. and Priyono, W.}, title = {Key to the Macaranga and Mallotus species (Euphorbiaceae) of east Kalimantan (Indonesia)}, journal = {Gardens Bull. Singapore}, year = {2000}, volume = {52}, pages = {11?87--11?87}, }
|Cannon, C. H. and Peart, D. R. and Leighton, M.
|Technical Comment: Tree species diversity in logged rainforest.
Vol. 284, pp. 1587a
@article{Cannon1998comment, author = {Cannon, C. H. and Peart, D. R. and Leighton, M.}, title = {Technical Comment: Tree species diversity in logged rainforest.}, journal = {Science}, year = {1999}, volume = {284}, pages = {1587a}, }
|Cannon, C. H. and Peart, D. R. and Leighton, M.
|Tree species diversity in commercially logged Bornean rainforest
Vol. 281, pp. 1366--1368
|Abstract:The effects of commercial Logging on tree diversity in tropical rainforest are Largely unknown. In this study, selectively logged tropical rainforest in Indonesian Borneo is shown to contain high tree species richness, despite severe structural damage. Plots logged 8 years before sampling contained fewer species of trees greater than 20 centimeters in diameter than did similar-sized unlogged plots. However, in samples of the same numbers of trees (requiring a 50 percent Larger area), Logged forest contained as many tree species as unlogged forest. These findings warrant reassessment of the conservation potential of large tracts of commercially Logged tropical rainforest.
@article{Cannon1998a, author = {Cannon, C. H. and Peart, D. R. and Leighton, M.}, title = {Tree species diversity in commercially logged Bornean rainforest}, journal = {Science}, year = {1998}, number = {5381}, volume = {281}, pages = {1366--1368}, }
|Cannon, C.H.
|The value of logged over forest
|Environmental Review
Vol. 5, pp. 8-14
@article{CannonER1998, author = {Cannon, C.H.}, title = {The value of logged over forest}, journal = {Environmental Review}, year = {1998}, number = {12}, volume = {5}, pages = {8-14}, }
|Slik, J. W. F.
|Keys to the taxa of Macaranga and Mallotus (Euphorbiaceae) of East Kalimantan (Indonesia)
|Flora Males. Bull
Vol. 12, pp. 157--178
@article{Slik1998, author = {Slik, J. W. F.}, title = {Keys to the taxa of Macaranga and Mallotus (Euphorbiaceae) of East Kalimantan (Indonesia)}, journal = {Flora Males. Bull}, year = {1998}, number = {4}, volume = {12}, pages = {157--178}, }
|Slik, J.W.F.
|Three New Malesian Species of Mallotus Section Hancea (euphorbiaceae)
Vol. 43, pp. 225--232
@article{SLIK1998, author = {Slik, J.W.F.}, title = {Three New Malesian Species of Mallotus Section Hancea (euphorbiaceae)}, journal = {BLUMEA}, year = {1998}, number = {1}, volume = {43}, pages = {225--232}, }
|Cannon, C. H. and Leighton, M.
|Comparative locomotor ecology of gibbons and macaques: is brachiation more efficient?
|Tropical Biodiversity
Vol. 3, pp. 261--267
@article{Cannon1996, author = {Cannon, C. H. and Leighton, M.}, title = {Comparative locomotor ecology of gibbons and macaques: is brachiation more efficient?}, journal = {Tropical Biodiversity}, year = {1996}, number = {3}, volume = {3}, pages = {261--267}, }
|Cannon, C. H and Leighton, M.
|Comparative locomotor ecology of gibbons and macaques - selection of canopy elements for crossing gaps
|American Journal of Physical Anthropology
Vol. 93, pp. 505--524
|Abstract:To examine functional questions of arboreal locomotor ecology, the selection of canopy elements by Bornean agile gibbons (Hylobates agilis) and long-tailed macaques (Macaca fascicularis) was contrasted, and related to locomotor behaviors. The two species, and in some cases, the macaque sexes, varied in their use of most structural elements. Although both species traveled most frequently in the main canopy layer (macaques: 56%, gibbons: 48%), the gibbons strongly preferred the emergent canopy layer and traveled higher than the macaques (31 vs. 23 m above ground) in larger trees (48 vs. 26 cm dbh). Macaques preferred to cross narrower gaps (50% were in the class 0.1-0.5 m wide) than gibbons (42% were 1.6-3.0 m wide), consistent with the maximum gap width each crossed (3.5 m for macaques, 9 m for gibbons). Macaques could cross only 12% of the gaps encountered in the main canopy, and < 5% of the gaps in each of the other four layers. In contrast, all layers appear relatively continuous for gibbons. Specialized locomotor modes were used disproportionately at the beginning and end of travel segments, further indicating that behavior was organized around gap crossings. A model is de?ned, the Perceived Continuity Index (PCI), which predicts the relative use of canopy strata for each species, based on the percentage of gaps a species can cross, the frequency of gaps, and median length of continuous canopy structure in each canopy layer. The results support the hypothesis that locomotor behaviors, and strategies of selecting canopy strata for travel, are strongly constrained by wide gaps between trees and are ultimately based on selection for e?icient direct line travel between distant points. (C) 1994 Wiley-Liss, Inc.
@article{Cannon1994, author = {Cannon, C. H and Leighton, M.}, title = {Comparative locomotor ecology of gibbons and macaques - selection of canopy elements for crossing gaps}, journal = {American Journal of Physical Anthropology}, year = {1994}, number = {4}, volume = {93}, pages = {505--524}, }
|Cannon, C. H and Peart, D. R and Leighton, M. and Kartawinata, K.
|The structure of lowland rainforest after selective logging in West Kalimantan, Indonesia.
|Forest Ecology and Management
Vol. 67, pp. 49--68
|Abstract:To quantify forest structure following mechanized selective logging in a dipterocarp forest in West Kalimantan, Indonesia, we compared unlogged forest and sites logged 6 months, 1 year and 8 years prior to sampling. Forty-one percent of the total area was in swamp forest, interdigitated with lowland forest. Small patches of lowland forest (15% of lowland area) and 85% of swamp forest escaped logging disturbance. The canopy of 76% of lowland forest was moderately to heavily disturbed by logging; 45% was in open gap or pioneer vegetation. There was only limited evidence of canopy development after 8 years. In lowland sites logged 6 months or 1 year before sampling, forest ?oor was disturbed in 16% of area by roads, tractor tracks and skid trails. Local canopy disturbance increased, but at a decreasing rate, with the amount of basal area extracted. Dipterocarp trees over 50 cm in diameter at breast height (DBH) comprised 70% of total basal area before logging. The harvest removed 62% of pre-cut dipterocarp basal area and 43% of pre-cut total basal area. Small dipterocarp trees (less than 50 cm DBH, below harvestable size) su?ered high mortality due to logging, possibly limiting future wood production. Logging resulted in a complex spatial mosaic of forest types and disturbance levels, suggesting options for conservation and management. Swamp forest timber resources, unharvested by conventional mechanized logging, could potentially be hand-logged by local villagers, increasing both villagers' incomes and revenue to concessions. Patches of unlogged forest may sustain some vertebrate and tree species. The detailed analysis of forest structure in this study provides part of the essential information needed to assess sustainability of management options. For the modeling of stand development that is necessary to develop an ecologically sound management system for dipterocarp forests in Indonesia, additional data on regeneration, tree growth and survival rates are required.
@article{Cannon1994a, author = {Cannon, C. H and Peart, D. R and Leighton, M. and Kartawinata, K.}, title = {The structure of lowland rainforest after selective logging in West Kalimantan, Indonesia.}, journal = {Forest Ecology and Management}, year = {1994}, volume = {67}, pages = {49--68}, }
|ENGELHARD, GH and SLIK, JWF
|On altitude dependent characters in Albinaria idaea(L. Pfeiffer, 1849), with a revision of the species(Gastropoda Pulmonata: Clausiliidae)
|Zoologische mededelingen
Vol. 68, pp. 21--38
@article{ENGELHARD1994, author = {ENGELHARD, GH and SLIK, JWF}, title = {On altitude dependent characters in Albinaria idaea(L. Pfeiffer, 1849), with a revision of the species(Gastropoda Pulmonata: Clausiliidae)}, journal = {Zoologische mededelingen}, year = {1994}, number = {1-14}, volume = {68}, pages = {21--38}, }
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