Danwei’s work on the Big-Mess-idae published as “Threatened Reef Corals of the World” in PLoS ONE

Huang Danwei is a DBS-supported graduate student (NUS-Overseas Graduate Scholar) at the Scripps Institution of Oceanography who is will defend his dissertation in August this year.

His work focuses mainly on the reconstruction and application of the coral evolutionary tree – reconstruction of the “Big-mess-idae” group and using trees to examine extinction risk and conservation status.

Huang Danwei

Danwei suggested this figure for a good summary of some of what the work has accomplished thus far:

This is from his paper published in PLoS ONE on 30 Mar 2012: Huang, D. 2012. D. PLoS ONE, 7(3): e34459. doi:10.1371/journal.pone.0034459

PLoS ONE_ Threatened Reef Corals of the World
It’s open-acess, hop over to read


“A substantial proportion of the world’s living species, including one-third of the reef-building corals, are threatened with extinction and in pressing need of conservation action. In order to reduce biodiversity loss, it is important to consider species’ contribution to evolutionary diversity along with their risk of extinction for the purpose of setting conservation priorities.

Here I reconstruct the most comprehensive tree of life for the order Scleractinia (1,293 species) that includes all 837 living reef species, and employ a composite measure of phylogenetic distinctiveness and extinction risk to identify the most endangered lineages that would not be given top priority on the basis of risk alone. The preservation of these lineages, not just the threatened species, is vital for safeguarding evolutionary diversity.

Tests for phylogeny-associated patterns show that corals facing elevated extinction risk are not clustered on the tree, but species that are susceptible, resistant or resilient to impacts such as bleaching and disease tend to be close relatives. Intensification of these threats or extirpation of the endangered lineages could therefore result in disproportionate pruning of the coral tree of life.”

The work hasn’t gone unnoticed – on 25 Apr 2012, this paper was identified by Nicholas Graham of James Cook University as a “must read” in the Faculty of 1000 (F1000) website. F1000 “identifies and evaluates the most important articles in biology and medical research publications. Articles are selected by a peer-nominated global ‘Faculty’ of the world’s leading scientists and clinicians [more than 10,000 experts worldwide] who then rate them and explain their importance.” ‘Approximately 2% of all published articles in the biological and medical sciences are listed each month.’

Threatened reef corals of the world. - F1000

“The author points out that linking evolutionary and extinction risk data may enable coral reef regions to be categorized for conservation based on species compositions that make the greatest contribution to evolutionary history. This may indeed be the case, but would ultimately need to be layered with other important ecological and social information that also needs to be considered in prioritizing conservation objectives.”

See: Graham N: “Danwei Huang combined phylogenetic distinctiveness data with International Union for Conservation of Nature (IUCN) extinction…” of: [Huang D. Threatened reef corals of the world. PLoS One. 2012; 7; doi: 10.1371/journal.pone.0034459]. Faculty of 1000, 25 Apr 2012. F1000.com/14267346#eval15779550

Thanks to Rudolf Meier for the alert!


Mei Lin and Kareen’s Giant Clam work aims to repopulate local reefs

Bid to repopulate giant clams on Singapore’s reefs by Jose Hong. The Straits Times, 21 Apr 2012. 

Newspaper giant clam proj 21042012 150dpi

BEFORE dawn broke last Monday, Ms Neo Mei Lin and Ms Kareen Vicentuan set off on a yacht from Sentosa on a 45-minute journey.

Taking advantage of the low spring tide, they anchored just off Terumbu Pempang Tengah, a submerged reef near the southern islands, before piloting a rubber dinghy onto the reef flat.

Their mission? To search for a creature once abundant in Singapore but now rarely seen – the giant clam.

Ms Neo, 25, a PhD student, and Ms Vicentuan, 31, a research assistant, both from the National University of Singapore (NUS), are part of a small team of biologists that wants to repopulate Singapore’s coral reefs with hundreds of giant clams, organisms which contribute to the reefs’ complexity.

But to do this, the biologists need to spawn clams of local origin. To do that, they first need to find them.

This project is funded by the National Parks Board, and its principal investigator, Dr Peter Todd, said that the results are important for Singapore’s marine biodiversity.

‘From the evidence of our research, we are certain that giant clams were once abundant in Singapore,’ said Dr Todd, 45, an assistant professor in the NUS’ department of biological sciences.

Old records dating back to the mid- 1850s indicate that the waters around Singapore used to have five species of giant clam, he said. In the 1950s, the clams could still be easily seen from the shore.

‘We have lost a lot of reefs, where the clams live, due to land reclamation. Furthermore, the waters around Singapore have more sediment in them than they used to, which reduces light penetration,’ Dr Todd explained.

‘As the clams photosynthesise, they need light, so that may have contributed to their decline.’

Another problem of sedimentation on the reefs, he added, was that it could cover up solid substrate, which clam larvae need to attach themselves to as they develop.

Lastly, he noted that the harvesting of clams for food likely contributed to their decline.

When Ms Neo surveyed 87,500 sq m of Singapore’s coral reefs in 2009 and 2010, she found only 59 individual clams of two species.

‘The aim of the project is to put back what we lost,’ said Dr Todd.

Last Monday, using GPS coordinates from previous expeditions, the two researchers found one small specimen of Tridacna squamosa, otherwise known as the fluted giant clam for the leaf-like projections on its shell, but left it alone as it was too young to breed. After another 20 minutes, they found another fluted giant clam large enough to be brought back to the Tropical Marine Science Institute on St John’s Island. Marking it, they went to look for others.

In the 11/2 hours of remaining low tide, two Tridacna crocea, otherwise known as the burrowing giant clam, were found, and their locations recorded. But when the tide came in, the duo returned to the marked fluted giant clam.

Soon, they separated the giant clam from its base and put it into a container, ready to be transported to the lab.

There, giant clams, some local and some from overseas, will be induced to breed, their offspring raised, and experiments conducted to see how they can be transplanted onto Singapore’s reefs.

It will, however, be a long time before the team knows if the placement of giant clams has been successful. Said Ms Neo: ‘Realistically, it will take seven to 10 years to know if this will work.’

But as long as giant clams can grow once again on the reefs, the team will be happy. ‘The wait will definitely be worth it,’ she said.”

Job: Full-time Research Assistant for Mangrove Propagule Dispersal project at NUS SDWA / Geography / Biological Sciences

Job: Full-time Research Assistant at NUS SDWA/Geography/Biological Sciences (Deadline: 15th May 2012)

The Singapore-Delft Water Alliance, National University of Singapore, is offering a full-time research assistant for the project “Mangrove Propagule Dispersal around Singapore and the Wider Thai-Malay Peninsula”. This is a joint project with the Department of Geography, Department of Biological Sciences, and the Singapore-Delft Water Alliance, National University of Singapore. The candidate will have the opportunity to work closely with National Parks Board staff and volunteers.

This position will be largely field-based. Tasks will include the monitoring of mangrove fruiting at sites in Singapore (including Sungei Buloh Wetland Reserve), and overseeing experiments on propagule flotation. Other mangrove research opportunities will also be available. The candidate should expect to spend a significant proportion of time in the field.

Requirements: Minimum of a Bachelors degree in Biological Sciences, Geography or similar field. The candidate must have adequate field experience, and must be confident and self-reliant in a field setting. Knowledge of mangroves is advantageous, though full training will be given.

This is a 12 month, full-time appointment, starting June/July 2012 (or earlier), with an expected salary of $3,000 per month, though may be higher depending on qualifications and experience.

Applications should include a letter of interest, a brief curriculum vitae and the contact details of two references. Please send applications to Dr. Daniel Friess at dan.friess@nus.edu.sg

For informal enquiries please contact:

Dr. Daniel Friess
Department of Geography
National University of Singapore

See also:

Deadline: 15th May 2012.

Richard Corlett leaves NUS for Xishuangbanna Tropical Botanical Garden, July 2012

Richard eating Durian in KL

Richard Corlett says,

“I will be leaving NUS and moving to the Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, at the beginning of July.

At XTBG I will be Director of a new ‘Center for Integrative Conservation’. My position will be generously funded under the national “One Thousand Foreign Experts Project”.

The Garden is at Menglun in SW Yunnan, near the borders with Laos and Myanmar, 96 km from Jinghong, the capital of the Xishuangbanna Dai Autonomous Prefecture. Jinghong is, in turn, an hour’s flight southwest from the provincial capital Kunming.

Despite the isolation, the Gardens supports a large community of researchers and state-of-the-art laboratories. It is also a world-class botanical gardens, with several square kilometres of collections open to visitors, as well as a large experimental area and some secondary rainforest and intact limestone forest.

There will be vacancies in the new Center for everything from graduate students through post-docs to professors, so if you know anyone who is interested in working there please point them in my direction.

The focus will be on conservation, largely but not exclusively of plants, and on SW China and the neighbouring countries. One of my roles will be to promote regional and international collaborations in conservation science and practice, and I would be happy to discuss potential projects any time.”

Job: Student field assistants wanted for plant traits in regenerating forests project

Title of project: Examining plant traits in regenerating forests
Job Description: Vegetation Survey Field Assistant

Position: Part time
Start date: Immediate
Frequency: about 3-4 times a week, until July-August 2012
Pay: $8/hour

Nature of work: Setting up vegetation plots in Central Catchment Nature Reserve, monitoring microenvironment, data entry.

Requirements: Must be able to hike comfortably in the forests and able to withstand long hours in the field.

Perks: Learn about forest plants, field techniques for surveying vegetaion and about tropical forest regeneration

Interested applicants, please contact CHUA Siew Chin at scchua@berkeley.edu