Understanding the historical biogeography of this global biodiversity hotspot is as important to long-term conservation goals as ecology and evolution are to understanding current patterns and processes. Today’s geography is, however, misleading and typical of only ~2% of the last million years; >90% of that time the region’s land area was 1.5–2.0 times larger as mean sea levels were 62 m below today’s, climates were cooler, and extensive forests and savanna covered the emerged Sunda plains. The region’s land area varied two-fold as sea levels fluctuated up to ±50 m with each of ~50 Pleistocene glacial cycles, and forests expanded and contracted with oscillations in land area and seasonality. This dynamic geographic history is relevant to the development of biogeographic regionalism and shows that it is today’s forests that are refugial, not those of the Last Glacial Maximum. This history affects how species will adapt or shift their ranges in response to global warming and further decreases in land area (submergence of low-lying coastal areas) during the 21st century. The alternative is mass species extinction. The biota is also threatened by the continued destruction of forest, destruction of Mekong River flood-pulse based ecosystems, and continued human population growth. Human biogeography will become more important in conservation planning as tens of millions of people who depend on protected area forests, riverine ecosystems, and coastal habitats become environmental refugees. Conservation scientists need to become more involved in regional ecological education, environmental stewardship, and ecosystem-based adaptation to sustain as much as possible of this rich biota and the ecological services it provides.

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Biogeography and conservation in Southeast Asia: how 2.7 million years of repeated environmental fluctuations affect today’s patterns and the future of the remaining refugial-phase biodiversity

The genus Dalbergia contains many valuable timber species threatened by illegal logging and deforestation, but knowledge on distributions and threats is often limited and accurate species identification difficult. The aim of this study was to apply DNA barcoding methods to support conservation efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically tested whether the markers could be used to solve taxonomic confusion concerning the timber species Dalbergia oliveri, and to identify the CITES-listed Dalbergia cochinchinensis. We also applied the barcoding markers to 14 samples of unknown identity. In general, we found that the barcoding markers discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri and encourage that this name is used consistently in Indochina. The CITES-listed Dalbergia cochinchinensis was successfully identified, and a species-specific assay can be developed from the data generated in this study for the identification of illegally traded timber. We suggest that the use of DNA barcoding is integrated into the work flow during floristic studies and at national herbaria in the region, as this could significantly increase the number of identified specimens and improve knowledge about species distributions.

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0138231&type=printable

The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.).

New Guinea is the world’s largest tropical island and has fascinated naturalists for centuries1,2. Home to some of the best-preserved ecosystems on the planet3 and to intact ecological gradients—from mangroves to tropical alpine grasslands—that are unmatched in the Asia-Pacific region4,5, it is a globally recognized centre of biological and cultural diversity6,7. So far, however, there has been no attempt to critically catalogue the entire vascular plant diversity of New Guinea. Here we present the first, to our knowledge, expert-verified checklist of the vascular plants of mainland New Guinea and surrounding islands. Our publicly available checklist includes 13,634 species (68% endemic), 1,742 genera and 264 families—suggesting that New Guinea is the most floristically diverse island in the world. Expert knowledge is essential for building checklists in the digital era: reliance on online taxonomic resources alone would have inflated species counts by 22%. Species discovery shows no sign of levelling off, and we discuss steps to accelerate botanical research in the ‘Last Unknown’8. A catalogue of the vascular flora of New Guinea indicates that this island is the most floristically diverse in the world, and that 68% of the species identified are endemic to New Guinea.

New Guinea has the world’s richest island flora

Plant diversity, forest dependency, and alien plant invasions in tropical agricultural landscapes

Southeast Asia was almost entirely covered by rainforest 8,000 years ago. Today, this region is experiencing the highest relative rates of deforestation and forest degradation in the humid tropics. Every year, millions of hectares of tropical forests are destroyed and degraded. Given the rapid rate of deforestation and the high concentration of endemic species in the region, Southeast Asia could lose 13–42% of local populations by the turn of the next century, at least 50% of which could represent global species extinction. In this Special Issue, we discuss the uniqueness of Southeast Asian biodiversity, drivers of forest destruction, threats to the region’s unique ecosystems and taxa, and key conservation challenges to provide a broad-based review of the science, management and policy issues concerning biodiversity conservation. Overall, we highlight the need for an interdisciplinary and multi-pronged strategy requiring all major stakeholders to work together to achieve the ultimate goal of reconciling biodiversity conservation and human well-being in the region.

Conserving Southeast Asia’s imperiled biodiversity: scientific, management, and policy challenges

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 α-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.

Biodiversity inventory and informatics in Southeast Asia

The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost-effective generation of high-quality sequence data has transformed many fields, including those focused on discovering species and surveying biodiversity, monitoring movement of biological materials, forensic biology, and disease diagnostics. There is a need to build capacity to generate useful sequence data in countries with limited historical access to laboratory resources, so that researchers can benefit from the advantages offered by these data. Commonly used molecular techniques such as DNA extraction, PCR, and DNA sequencing are within the reach of small laboratories in many countries, with the main obstacles to successful implementation being lack of funding and limited practical experience. Here we describe a successful approach that we developed to obtain DNA sequence data during a small DNA barcoding project in Indonesia.

https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.1002/aps3.1167

Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia.

Research on feed plants selection and nesting site of cuscus (Phalanger sp.) was conducted in Nature Reserve of Gunung Mutis, West Timor, East Nusa Tenggara. The study was done in the montane rain forest with the altitude of 1530-2010 m a.s.l. The results showed seven species of plants was selected by cuscus as their nesting site and 41 species of plants as their feed resources. Parts of the plants being consumed were young leaves, flower, and fruit. Their habitat was damaged caused by exploitation of the forest. Meanwhile, hunting pressure by local people to provide their meat supply threatens the existence of cuscuses.Â© 2005 Jurusan Biologi FMIPA UNS SurakartaKeywords: Phalanger sp., cuscus, plant, feed, nesting site, Gunung Mutis, East Nusa Tenggara.

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Feed Plants Selection and Nesting Site of Cuscus (Phalanger sp.) in Nature Reserve of Gunung Mutis, East Nusa Tenggara

Vegetation analysis of trees in Harapan Rainforest, PT.REKI, Jambi, was conducted on October-November 2009. Two 50m x 100m (0,5 ha) plots were established to obtain primary data for analysis. Plot one was made in the area of Medium Secondary Forest and plot two in the area of High Secondary Forest. Results shows that, the number of tree species were recorded from the two plots was 205 species from 550 individual trees with a total Basal Area (BA)= 64.75 m2. Plot one has 123 species from 284 individuals with BA = 10.82 m2 and Diversity Index (H')= -1.87. Bellucia axinanthera was recorded as the dominant species with Importance Value (IV)= 37.21%. Meanwhile, plot two has 126 species from 266 individuals with BA= 53.93 m2 and (H')= -1.97. Shorea acuminata was recorded as the dominant species with IV= 12.93%. Plot two (High Secunder Forest) has higher diversity of tree species than plot one (Medium Secunder Forest).The structure and composition of vegetation between plot one and plot two is different with similarity index for the two plots is only 21.46%.

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Analisis Vegetasi Pohon Di Hutan Hujan Tropik Harapan, Jambi [Vegetation Analysis of Trees in Harapan Rainforest, Jambi]

Indonesia is one of the world’s biodiversity hotspots. It is estimated to be the home of 9.5% flowering plant species, making it the seventh country with the highest biodiversity. Plant data collection is necessary to ascertain the level of plant biodiversity, as such data help in conservation efforts and long-term management. One of the methods applied is the collection of plants, with the purpose to acquire as much data about its biological resources. The collected specimen are then gathered and processed into a herbarium to be used as an information source in managing biological resources. Unfortunately, there are some difficulties related to the making and management of a herbarium. Digital herbarium are one of the potential solutions to the limitations of the traditional herbarium. It is a collection of plant pictures, replete with every step of productivity (leaf, flower, fruit) and the main characteristics of the plant species. It is an effective method for the identification and collection of plant biodiversity in Indonesia. About 2149 plants have been gathered from Borneo, Seram, Waigeo, Flores and Sulawesi which consisted of 152 family, 512 genus, and 1,832 species, with a total of 30391 pictures of plant parts. From the experiment conducted on 672 specimens, it achieved 98.8 % accuracy on the family level and 80.1 % accuracy on the genus level, while the species level reached 78.8%. The results showed that digital herbarium can be used to conduct identification and data collection of plant biodiversity. Furthermore, this method is simple, cheap and relatively easier to conduct. The output is a catalog of plant species in specific areas, which provides better understanding about plant identification and biodiversity, enhances conservation practices, and provides better long-term protection for Indonesian plant biodiversity.

http://journal.uin-alauddin.ac.id/index.php/biogenesis/article/download/15697/pdf

Teguh Triono

Papers

Biodiversity inventory and informatics in Southeast Asia

Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia.

Feed Plants Selection and Nesting Site of Cuscus (Phalanger sp.) in Nature Reserve of Gunung Mutis, East Nusa Tenggara

Analisis Vegetasi Pohon Di Hutan Hujan Tropik Harapan, Jambi [Vegetation Analysis of Trees in Harapan Rainforest, Jambi]

The Digital Herbarium: Solutions for Data Collection and Identification of Indonesian Plant Diversity