The extraordinary species richness and endemism of the Indo-Australian Archipelago (IAA) exists in one of the most geologically dynamic regions of the planet. The provenance of its biota has been debated, particularly in the area known as Wallacea. Application of molecular genetic approaches and a better understanding of the region's complex geology have stimulated much recent biogeographic work in the IAA. We review molecular phylogenetic and phylogeographic studies in light of current geological evidence. Present distribution patterns of species have been shaped largely by pre-Pleistocene dispersal and vicariance events, whereas more recent changes in the connectivity of islands within the Archipelago have influenced the partitioning of intraspecific variation. Many genetic studies have uncovered cryptic species with restricted distributions. We discuss the conservation significance of the region and highlight the need for cross-taxon comparative studies using newly developed analytical approaches well suited to the challenges of historical inference in this region.

Indonesia is one of the ten member states of the economically and politically diverse regional organization of the Association of Southeast Asian Nations (ASEAN). Southeast Asia comprises four of the 25 global biodiversity hotspots, three of the 17 global megadiverse countries (Indonesia, Malaysia, and the Philippines) and the most diverse coral reefs in the world. All member states are Parties to the Convention on Biological Diversity (CBD). We discuss ASEAN-wide joint activities on nature conservation and sustainable use of biodiversity that do not stop at national borders.The Indonesian archipelago comprises two of the world’s biodiversity hotspots (areas with a high degree of endemic species that are highly threatened by loss of habitats): Its insular character and complex geological history led to the evolution of a megadiverse fauna and flora on the global scale. The importance of biodiversity, e.g., in traditional medicine and agriculture, is deep-rooted in Indonesian society. Modern biodiversity pathways include new fields of application in technology, pharmacy and economy along with environmental policies. This development occurred not only in Indonesia but also in other biodiversity-rich tropical countries.This review summarizes and discusses the unique biodiversity of Indonesia from different angles (science, society, environmental policy, and bioeconomy) and brings it into context within the ASEAN region. The preconditions of each member state for biodiversity-related activities are rather diverse. Much was done to improve the conditions for biodiversity research and use in several countries, primarily in those with a promising economic development. However, ASEAN as a whole still has further potential for more joint initiatives. Especially Indonesia has the highest biodiversity potential within the ASEAN and beyond, but likewise the highest risk of biodiversity loss.We conclude that Indonesia has not taken full advantage of this potential yet. A growing national interest in local biodiversity as a natural resource is a welcome development on one hand, but the risk of too many restrictions for, e.g., the science community (high level of bureaucracy at all project stages from planning phase, visa procedures, field work permits, scientific exchange and project managment issues, governmental budget cuts for basic research and restricted access to international literature for Indonesian researchers) does significantly hamper the internationalization of biodiversity-related science. In the long run, Indonesia has to find a balance between protectionism and sensible access to its national biodiversity to tackle global challenges in biodiversity conservation, health issues, food security, and climate change.

Biotic Evolution and Environmental Change in Southeast Asia - edited by David Gower July 2012