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.

Aim The Lesser Sunda Islands are situated between the Sunda and Sahul Shelves, with a linear arrangement that has functioned as a two‐way filter for taxa dispersing between the Asian and Australo‐Papuan biogeographical realms. Distributional patterns of many terrestrial vertebrates suggest a stepping‐stone model of island colonization. Here we investigate the timing and sequence of island colonization in Asian‐origin fanged frogs from the volcanic Sunda Arc islands with the goal of testing the stepping‐stone model of island colonization. Location The Indonesian islands of Java, Lombok, Sumbawa, Flores and Lembata. Taxon Limnonectes dammermani and L. kadarsani (Family: Dicroglossidae) Methods Mitochondrial DNA was sequenced from 153 frogs to identify major lineages and to select samples for an exon‐capture experiment. We designed probes to capture sequence data from 974 exonic loci (1,235,981 bp) from 48 frogs including the outgroup species, L. microdiscus. The resulting data were analysed using phylogenetic, population genetic and biogeographical model testing methods. Results The mtDNA phylogeny finds L. kadarsani paraphyletic with respect to L. dammermani, with a pectinate topology consistent with the stepping‐stone model. Phylogenomic analyses of 974 exons recovered the two species as monophyletic sister taxa that diverged ~7.6 Ma with no detectable contemporary gene flow, suggesting introgression of the L. dammermani mitochondrion into L. kadarsani on Lombok resulting from an isolated ancient hybridization event ~4 Ma. Within L. kadarsani, the Lombok lineage diverged first while the Sumbawa and Lembata lineages are nested within a Flores assemblage composed of two parapatrically distributed lineages meeting in central Flores. Biogeographical model comparison found strict stepping‐stone dispersal to be less likely than models involving leap‐frog dispersal events. Main conclusions These results suggest that the currently accepted stepping‐stone model of island colonization might not best explain the current patterns of diversity in the archipelago. The high degree of genetic structure, large divergence times, and absent or low levels of migration between lineages suggests that L. kadarsani represents five distinct species.

(a) A map of Wallacea showing islands invaded by Duttaphrynus melanostictus in red, islands inhabited by Varanus komodoensis in blue, and localities of genetic samples in yellow points. (b) A D. melanostictus from Lombok Island. (c) Environmental niche model for the Sunda Islands clade of D. melanostictus projected into Wallacea. Green color indicates very high suitability, yellow color indicates high suitability, and orange color indicates moderate suitability.

The genus Trimeresurus comprises a group of venomous pitvipers endemic to Southeast Asia and the Pacific Islands. Of these, Trimeresurus insularis, the White-lipped Island Pitviper, is a nocturnal, arboreal species that occurs on nearly every major island of the Lesser Sunda archipelago. In the current study, venom phenotypic characteristics of T. insularis sampled from eight Lesser Sunda Islands

The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal. Cryptoblepharus species that occur in coastal habitats have on average dispersed 13 to 14 times more frequently than non-coastal species and coastal specialization has, therefore, led to an extraordinarily widespread distribution that includes multiple continents and distant island archipelagoes. Furthermore, their presence across the Pacific substantially predates the age of human colonization and we can explicitly reject the possibility that these patterns are solely shaped by human-mediated dispersal. Overall, by combining new analytical methods with a comprehensive phylogenomic dataset, we use a quantitative framework to show how coastal specialization can influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.