Sundaland Dipterocarp forests during Quaternary glacial maxima
22 Nov 2014
In findings published in the Proceedings of the National Academy of Sciences (U.S.A.), the persistence of Dipterocarp forests on the greatly expanded Sunda Shelf during the brief glacial maxima of the Quaternary Period was supported by the largest database of collections of Dipterocarpaceae specimens in the world and advanced niche modeling techniques. The team of scientists, including Drs. Cannon and Slik (both formerly at XTBG), expand the evidence that strongly suggests that the current Southeast Asian forests have been greatly fragmented and reduced in their extent, although forests of the glacial maxima might have been less species-rich with many species having smaller geographic distributions. Most importantly, current forests must have experienced a great deal of mixture and migration from the slightly drier and cooler conditions of the Last Glacial Maximum which ended roughly 12,000 years ago. Little evidence was found for the existence of a savanna region on any substantial portion of the Sunda Shelf.
Genomic data reveals patterns in the regulation of transpiration in Ficus
22 Oct 2014
Protein Domain Analysis of Genomic Sequence Data Reveals Regulation of LRR Related Domains in Plant Transpiration in Ficus. Tiange Lang, Kangquan Yin, Jinyu Liu, Kunfang Cao, Charles H. Cannon, and Fang K. Du. PLoS One.
Predicting protein domains is essential for understanding a protein’s function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated withde novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.
Borneo and Indochina are evolutionary hotspots
18 Oct 2014
A recent publication in Systematic Biology highlights the role of Borneo and Indochina as exceptional evolutionary hotspots in Southeast Asia. Compiling and reanalyzing a large amount of data, a team of 13 experts representing a wide range of scientific fields demonstrate that for a diverse range of fauna and flora, within-area diversification and subsequent emigration have been the predominant signals characterizing Indochina and Borneo’s biota since at least the early Miocene. Dr. Cannon participated in this study and was a co-author on the publication.
The pdf is available for free download from http://sysbio.oxfordjournals.org/content/63/6/879.full.pdf+html
Dr. Cannon speaks at evolutionary genomics meeting
15 Oct 2014
Dr. Charles Cannon gave an invited presentation at the “Evolutionary Genetics and Genomics” workshop at Cold Spring Harbor, Asia in Suzhou, China on Oct 10, 2014. His talk was entitled “Tropical Diversification and Genomic Mutualisms”.
The workshop site is at the following link: https://www.csh-asia.org/2014meetings/Genome.html
While in China, he was also invited to make a presentation at Sun Yat Sen University in Guangzhou, China. His talk was entitled “See the forest through the trees” and was given to the research groups of Prof. Chung-I Wu and Prof. Suhua Shi.
Peter Alele publishes study on soils in Uganda
15 Oct 2014
How Does Conversion of Natural Tropical Rainforest Ecosystems Affect Soil Bacterial and Fungal Communities in the Nile River Watershed of Uganda?
- Published: August 12, 2014
- DOI: 10.1371/journal.pone.0104818
Footprints of divergent selection in tropical chestnut
17 Aug 2014
Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)
, , and
Given predicted rapid climate change, an understanding of how environmental factors affect genetic diversity in natural populations is important. Future selection pressures are inherently unpredictable, so forest management policies should maintain both overall diversity and identify genetic markers associated with the environmental factors expected to change most rapidly, like temperature and rainfall. In this study, we genotyped 648 individuals in 28 populations of Castanopsis fargesii (Fagaceae) using 32 expressed sequence tag (EST)-derived microsatellite markers. After removing six loci that departed from Hardy–Weinberg equilibrium, we measured genetic variation, population structure and identified candidate loci putatively under selection by temperature and precipitation. We found that C. fargesii populations possessed high genetic diversity and moderate differentiation among them, indicating predominant outcrossing and few restrictions to gene flow. These patterns reduce the possible impact of stochastic effects or the influence of genetic isolation. Clear footprints of divergent selection at four loci were discovered. Frequencies of five alleles at these loci were strongly correlated with environmental factors, particularly extremes in precipitation. These alleles varied from being near fixation at one end of the gradient to being completely absent at the other. Our study species is an important forest tree in the subtropical regions of China and could have a major role in future management and reforestation plans. Our results demonstrate that the gene flow is widespread and abundant in natural populations, maintaining high diversity, while diversifying selection is acting on specific genomic regions.
Field Methods in Tropical Ecology, Evolution, and Conservation – north Sulawesi, Indonesia
26 Jul 2014
Dr. Cannon taught in a field course organized by Myron Shekelle and Maryati Abiduna. The course was funded primarily by the Ewha Woman’s University of South Korea.
Genome size variation in Fagaceae and its implications for trees
23 Jul 2014
CHEN Sichong, now pursuing a PhD at the University of New South Wales with Angela Moles, has published her research on genome size variation in the Fagales in the journal Tree Genetics and Genomes.
Polyploidization is a major source of diversification among plants, particularly during cladogenesis, but most evidence involves herbaceous temperate species. The prevalence of polyploidy among woody taxa is largely unknown, especially among tropical groups. In this study, we examined genome size variation globally and at several taxonomic levels within the Fagaceae. This family has diversified in the northern temperate zone (Quercus) and at least twice in the Asian tropics (Lithocarpus andCastanopsis), allowing us to examine genomic size evolution across a broad latitudinal range. We compared nuclear DNA contents from 78 species in six genera, including new measurements for 171 individuals from 47 Chinese species using standard flow cytometry methods. No evidence suggests that polyploidization or whole genome duplication has occurred in the family. Genome size varied among genera, but limited variation was present in each genus and species. In general, tropical species had larger genomes than temperate species, but the ancestral state cannot be determined given current evidence. Partial duplication does seem to occur among species as within genus variation was larger than within species variation. A review of the literature suggests that genome size and even chromosome structure is highly conserved among woody plants and trees. We propose that ploidy level and genome size are conserved among trees because they participate in diverse syngameons. This behavior would provide similar benefits to polyploidization but avoid exclusion from the syngameon. This conservatism in genome size and structure should enhance ongoing whole genome studies.
Dr. Yi Zhuangfang publishes another paper concerning the ecological economics of forests in Xishuangbanna
25 Feb 2014
Can carbon-trading schemes help to protect China’s most diverse forest ecosystems? A case study from Xishuangbanna, Yunnan
authors: Zhuang-Fang Yi , Grace Wong, Charles H. Cannon, Jianchu Xu, Philip Beckschäfer, and Ruth D. Swetnamg
published in Land Use and Policy
Xishuangbanna has been largely transformed from biodiverse natural forests and mixed-use farms into monoculture rubber plantations in just twenty years. This conversion has expanded into forests previously protected by the community and onto marginal sites at high-elevation. Market-based ecosystem payments, especially carbon financing, are potential tools to prevent further forest loss in China. Here, we compare rubber net present value (NPV), carbon sequestration, and seed-plant species diversity for Xishuangbanna given three land-use scenarios: Business-As-Usual (BAU), Economic Oriented Scenario (EOS) and Conservation Oriented Scenario (COS) using a previously published spatial map of rubber profitability. The EOS achieved the greatest rubber profit but caused substantial reductions in natural forest area, biodiversity and carbon stocks. The EOS also requires substantial immigration of workers into a remote and ecologically important region with little social infrastructure for basic security, food security, health-care and education, causing frequently ignored costs. As expected, the COS will maintain the highest levels of natural forest area, sequester 57% more carbon, and 71% more biodiversity than EOS. Given the conservation value of the carbon stores and rich biodiversity residing in Xishuangbanna’s natural forests, reducing rubber NPV only marginally would probably cost less than attempting to recover these resources. We recommend that rubber plantations be limited to established, productive lowland areas whilst protecting intact high-elevation forest and reforesting low-productivity plantations. These actions will enhance carbon sequestration and biodiversity conservation. Management policies focused solely on profits, like the EOS scenario, will fail to sustain the entire range of natural resources and ecosystem services. The prices in the carbon market would have to be considerably larger than they are currently to compete with the profitability of rubber.
Official press release by PhytoKeys: A new species of Oak hidden away in the greenery of Ton Pariwat Wildlife Sanctuary
14 Feb 2014
>> An international team of scientists from Xishuangbanna Tropical Botanical Garden (China) and the Forest Herbarium (BKF – Thailand) discovered a new species of Stone Oak in the Ton Pariwat Wildlife Sanctuary in Thailand. This isolated sanctuary is popular for its rich bird- and wildlife such as the Blue-banded Kingfisher and Whitehanded Gibbons, as well for its rare and beautiful flora like Rafflesia’s – known to hold some of the largest flowers on earth. The wildlife sanctuary covers a region of low-lying forested mountains and is located in the middle of a fascinating transition zone that lies between the northern Indochinese and the southern Sundaland biogeographic regions. A recent addition to the endemic species of this area is the newly described species of Stone Oak, currently known only from the sanctuary.
The new species Lithocarpus orbicarpus is a medium to small tree with simple leaves. It can be easily distinguished by its spherical acorns covered with a dense pattern of irregularly placed scales that completely conceal the nut, except for a tiny opening at the top, and which are arranged in dense clusters on upright spikes.
“This species is only known from Thailand, and has not been recorded outside Ton Pariwat Wildlife Sanctuary. During our field survey, we found only one individual tree, located on a gentle sloping section of closed dense forest,” explains one of the authors Dr. Strijk. “We know next to nothing about this species’ biology, it’s evolution or it’s position within the Oak family. Follow-up molecular work will provide us with more information, but additional survey work will have to be undertaken to determine the actual population size within the sanctuary. So far, it seems that the species is not only endemic but also very rare within the confined area where it appears.”
Such distribution limitation and rarity is not uncommon in tropical Oaks. Within this region alone, there are several species that are known only from one or two localities. Though not uncommon, such restricted ranges stress the possible delicate conservation status of new species and other flora and fauna present in the Ton Pariwat Wildlife Sanctuary. “The unique species composition, high diversity and relatively intact forest structure underscore the importance of strengthening ongoing and future conservation measures at Ton Pariwat Wildlife Sanctuary, as a key element of wider conservation efforts in southern Thailand,” adds Dr. Strijk.
Currently, more than 300 species of Stone Oak have been described, occurring from eastern India to Japan and the eastern tip of Papua New Guinea. The fieldwork and surveys in Ton Pariwat Wildlife Sanctuary by the team of Dutch and Thai botanists are part of ongoing research on the genomics, systematics, biogeography and evolution of tropical Asian Oaks and their close relatives.<<
Original press release here: LINK
Original Source and citation:
Strijk JS, Sirimongkol S, Rueangruea S, Ritphet N, Chamchumroon V (2014) Lithocarpus orbicarpus (Fagaceae), a new species of Stone Oak from Phang Nga province, Thailand. PhytoKeys 34: 33. doi: 10.3897/phytokeys.34.6429
All images © 2013-2014 S.Sirimongkol & J.S.Strijk
Free downloads until Mar 26th of Dr. Yi’s Ecological Indicators paper
10 Feb 2014
Elsevier Press is offering a personal link for sharing our new article “Developing indicators of economic value and biodiversity loss for rubber plantations in Xishuangbanna, southwest China: A case study from Menglun township” in Ecological Indicators:
This link will provide free access to your article, and is valid for 50 days, until 26th March, 2014.
Get it while it’s free!!
Dr. Strijk and co-authors describe a new species of Stone Oak from Phang Nga province, Thailand
8 Feb 2014
In close collaboration with botanists from Thailand’s Forest Herbarium (BKF) (LINK), Dr. Strijk has described a new species of Lithocarpus collected from Phang Nga Province in the Peninsular Floristic Region of Thailand. Included in the manuscript are the first technical illustrations and colour photographs of the new species, as well as a description of its conservation status and the collecting locality. In addition, an amendment to the existing diagnostic key to Thai Lithocarpus is included, and important differences with morphologically similar species found in Thailand and the surrounding region are discussed.
The manuscript has been published in the journal PhytoKeys and can be accessed for free on the journal homepage: doi: 10.3897/phytokeys.34.6429
Citation: Strijk, J.S., Sirimongkol, S., Rueangruea, S., Ritphet, N. and Chamchumroon., V. 2014. Lithocarpus orbicarpus (Fagaceae), a new species of Stone Oak from Phang Nga province, Thailand. PhytoKeys 34: 33–45. doi: 10.3897/phytokeys.34.6429
All images © 2013-2014 J.S.Strijk
Signs of Change: crowd-sourcing time-lapse photography
6 Feb 2014
A new crowd-funding effort has just launched at experiment.com, organized by the great people at the SciFund Challenge.
Check out my proposal: https://experiment.com/projects/signs-of-change-documenting-environmental-change-using-crowd-sourced-time-lapse-photography or microryza.com/signsofchange.
The idea is to create sites where anyone can snap a photo of the landscape from a fixed position and contribute to a time-lapse movie of the location. In this way, we can monitor environmental change together, watch the seasons change, see the effect of management and natural events, like fires or droughts. The idea is a simple but exciting one. Please consider contributing, even small amounts can help get this idea started!
Timing and tempo of evolutionary diversification in a biodiversity hotspot: Dr. Strijk publishes a study on Indian Ocean Island Primulaceae
24 Jan 2014
Dr. Joeri Strijk and co-authors have completed a study on the phylogenetic relationships and spatio-temporal diversification in Indian Ocean Primulaceae, assessing correlations between speciation rates, geographical expansion and ecomorphological specialization. Primulaceae on Madagascar and Indian Ocean Islands consist primarily of the genera Badula and Oncostemum.
Phylogenetic analyses were conducted 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. In addition, parametric ancestral area reconstruction was performed, 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.
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.
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.
The article is available on the Journal of Biogeography webpage. Click here
Citation: – Strijk, J.S., Bone, Thébaud, C., Buerki, S., Fritsch, P.W., Hodkinson, T.R. and Strasberg, D. 2013. Timing and tempo of evolutionary diversification in a biodiversity hotspot: Primulaceae on Indian Ocean islands. Journal of Biogeography 41(4), 810–822. doi: 10.1111/jbi.12259
Photographs by R.E.Bone (©2013)
Historical Biogeography of Macaranga and Mallotus – Dr. Strijk co-authors a study on comparative molecular dating in Euphorbiaceae
24 Jan 2014
Together with researchers from the Naturalis Biodiversity Center and Leiden University (the Netherlands), Dr. Strijk reconstructed and analyzed two large molecular generic datasets for Macaranga and Mallotus (Euphorbiaceae), using Bayesian relaxed clock analyses. Using different molecular markers, multiple fossil calibrations and varying sample sets between the two genera, we reconstructed their evolutionary history and the timing and geographical pattern of their diversification. We compared patterns of dispersal and diversification between Macaranga and Mallotus using ancestral area reconstruction in RASP and contrasted results with biogeographical and geological records to assess accuracy of inferred age estimates.
Macaranga and Mallotus show a high degree of temporal and geographical synchronicity in dispersal events. To some extent, this is to be expected, as the genera share very similar ecological strategies, have similar geographical distributions and a recent common ancestry, potentially leading to exposure and diversification under comparable biotic and abiotic conditions. In our study design, we paid particular attention to assemble DNA sequence data sets for Macaranga and Mallotus that were highly dissimilar. Confidence in biogeographical reconstruction and inferred, concordant dispersals increases when large-scale congruence exists in molecular dating results between such data sets.
We find that inferred dispersal events closely match known geological configurations and previously described dispersal pathways.Our results are also 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. Eventhough there is a high degree of congruence, the overall mode and tempo of dispersal and diversification differ significantly as shown by distribution patterns of extant species. Our study shows that concordant evolution with closely related species rich groups of Euphorbiaceae can progress rapidly, over large distances and in widely differing environments.
Link to open access publication at PLoS ONE: LINK
Citation: – Van Welzen, P.C., Strijk, J.S., Van Konijnenburg-van Cittert, J.H.A., Nucete, M. and Merckx, V.S.F.T. 2014. Dated Phylogenies of the Sister Genera Macaranga and Mallotus (Euphorbiaceae): Congruence in Historical Biogeographic Patterns? PLoS ONE 9(1): e85713. doi: 10.1371/journal.pone.0085713
Topics in Tropical Asian Forestry: technology meets conservation – applications being accepted now!
25 Sep 2013
Topics in Tropical Asian Forestry: technology meets conservationApplications for full scholarships are now being accepted until Nov. 15, 2013! For a full course description and instructions on how to apply, please visit the “Training” tab on this site.
“Magic” mushrooms observed in Xishuangbanna
8 Sep 2013
Taylor Lockwood, professional mushroom photographer and official media specialist for the NSF-NSFC field course in digital forestry techniques, discovered a previously unreported bio-luminescent mushroom growing in XTBG. Read the full report at the following link:
Dr. Cannon presents at Flora Malesiana IX in Bogor, Indonesia
8 Sep 2013
Dr. Cannon made two presentations at the Ninth meeting of the Flora Malesiana project: “Near-sensing tropical Asian forests” and “Land area dynamics of the Southeast Asian archipelago during the Quaternary Period”. The meeting was held from Aug 27-31, 2013 in Bogor, Indonesia.
Song of the near-sensing tribe
24 Aug 2013
Click on the link below and listen to the rhythmic but primitive farewell song of the near-sensers in their native habitat (which is everywhere).
Rainforest party jamz
Topics in Tropical Asian Forestry field course underway
10 Aug 2013
The field course on “Near-sensing and forest monitoring techniques” has now finished its second week and the students are busy working on their independent projects. Part of the Topics in Tropical Asian Forestry course, jointly funded by the U.S. National Science Foundation and the Natural Science Foundation of China, the course is being held from July 26 until Aug 21, 2013. The course is led by Dr. Chuck Cannon (XTBG-Texas Tech) and Dr. Dave Lohman (City University New York) and is attended by 28 students from the USA. China, and seven other countries.
Guest speakers have included Dr. Luo Shu-jin (Beijing University), Dr. Doug Yu (KIZ-Univ East Anglia), Dr. He Fangliang (Univ. Alberta-Sun Yat-Sen Univ), Dr. Richard Corlett (XTBG), Dr. Ferry Slik (XTBG), Dr. Doug Schaefer (XTBG), Dr. Chen Jin (XTBG), Dr. Chen Hui (XTBG) and Mr. Wang Ximin (XTBG). We will be making an announcement about how to apply for next year’s course shortly!
The group after the culture show in Jinghong! The dancing elephants with the water pipes were the best!