The genus Agrioglypta Meyrick (Lepidoptera: Crambidae, Spilomelinae) from Indonesia with descriptions of three new species

Inventory studies on the genus Agrioglypta Meyrick, 1932 have been conducted in Java, Sulawesi, and Papua during 2007-2011. This study also aims to explore the diversity of Agrioglypta in Indonesia, and the possible apomorphic characteristics, especially genitalic characters, that support the monophyly of the genus. Three new species were discovered, A. hastantiae sp. nov., A. ubaidillahi sp. nov., and A. halimunensis sp. nov., for a total of nine species of the genus recorded in Indonesia. Images of adults and genitalia are provided for all new species.

Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)

Despite many attempts in the Sanger sequencing era, the phylogeny of fig trees remains unresolved, which limits our ability to analyze the evolution of key traits that may have contributed to their evolutionary and ecological success. We used restriction-site-associated DNA sequencing (c. 420 kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus. To increase phylogenetic information for higher-level relationships, we targeted conserved regions and assembled paired reads into long loci to enable the retrieval of homologous loci in outgroup genomes. We compared morphological and molecular results to highlight discrepancies and reveal possible inference bias. For the first time, we recovered a monophyletic subgenus Urostigma (stranglers) and a clade with all gynodioecious Ficus. However, we show, with a new approach based on iterative principal component analysis, that it is not (and will probably never be) possible to homogenize evolutionary rates and GC content for all taxa before phylogenetic inference. Four competing positions for the root of the molecular tree are possible. The placement of section Pharmacosycea as sister to other fig trees is not supported by morphological data and considered a result of a long-branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides Ficus into monoecious versus gynodioecious species appears most plausible. It seems most likely that the ancestor of fig trees was a freestanding tree and active pollination is inferred as the ancestral state, contrary to previous hypotheses. However, ambiguity remains on the ancestral breeding system. Despite morphological plasticity, we advocate restoring a central role to morphology in our understanding of the evolution of Ficus, as it can help detect systematic errors that appear more pronounced with larger molecular datasets.

A tiny new species of Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) from Belitung Island and Southeastern Sumatra, Indonesia

A tiny new species of narrow-mouthed frog of the genus Microhyla is described from the island of Belitung and southeastern Sumatra, Indonesia. The most distinctive feature of the new frog is its diminutive adult size, snout-vent length ranging only from 12.3 to 15.8 mm in adult males. Phylogenetic analyses based a fragment of the mitochondrial 16S rRNA gene, along with detailed morphological and acoustic comparison differentiate the new taxon from all known congeners. The new species, formally described as Microhyla sriwijaya sp. nov., is a member of the M. achatina species group and the sister taxon to M. orientalis. It is diagnosable from other congeners by a combination of characters: (1) smaller male snout-vent size 16 mm; (2) snout obtusely rounded in dorsal view; (3) absence of mid-dorsal line and skin fold; (4) first finger reduced (finger I length less than half of finger II length); (5) dorsum with a prominent dark median mark extending posteriorly, narrow anteriorly near the level of the shoulder and expanding dorsolaterally up to the vent; margins of the dorsal marking concave with broad reddish-brown or orange colouration on either side; (6) foot webbing rudimentary, reaching just up to the first subarticular tubercle on all toes; (7) dorsal skin with prominent tubercles, especially in life; (8) tibiotarsal articulation of adpressed limb reaching beyond the snout tip; and (9) males produce a single type of call with pulsatile temporal structure, calls of relatively short duration ranging between 31.862.8 s, with two to three pulses delivered at a rate ranging between 32.236.0 pulses per second, and the mean overall dominant frequency of 4.3 kHz. The uncorrected pairwise genetic distances between Microhyla sriwijaya sp. nov. and all other known congeners are > 3.8% for the studied 16S gene fragment. The new species was discovered from wayside rural areas with oil palm plantations at four localities in the small island of Belitung (type locality), and from coffee plantation and secondary forest at Lampung in southeastern Sumatra. It is not known from any protected area and appears to be threatened due to tin mining activity, intensive logging, oil palm, and other commonly practiced agriculture activities.

Homogeneity and Possible Replacement of Populations of the Dengue Vectors Aedes aegypti and Aedes albopictus in Indonesia

Currently, Aedes aegypti, the principal vector of dengue virus in Indonesia, has spread throughout the archipelago. Aedes albopictus is also present. Invasion and high adaptability of the Aedes mosquitoes to all of these areas are closely related to their ecology and biology. Between June 2016 and July 2017, larval and adult mosquito collections were conducted in 43 locations in 25 provinces of Indonesia using standardized sampling methods for dengue vector surveillance. The samples collected were analyzed for polymorphism and phylogenetic relationship using the mitochondrial cox1 gene and the nuclear ribosomal internal transcribed spacer 2 (ITS2). Almost all Ae. aegypti samples collected in this study (89%) belonged to the same haplotype. A similar situation is observed with the nuclear ITS2 marker. Populations of Ae. aegypti characterized few years ago were genetically different. A closely related observation was made with Aedes albopictus for which the current populations are different from those described earlier. Ae. aegypti populations were found to be highly homogenous all over Indonesia with all samples belonging to the same maternal lineage. Although difficult to demonstrate formally, there is a possibility of population replacement. Although to a lower extent, a similar conclusion was reached with Ae. albopictus.

Eusocial wasp fauna of Sulawesi Island, the central island of Wallacea (Hymenoptera: Vespidae; Polistinae, Vespinae)

Taxonomy of eusocial wasps (Polistinae and Vespinae) occurring in Sulawesi Island, the central island of Wallacea, is reviewed. Sixteen (12 polistine and four vespine) species are recognized. Polistes (Polistella) stigma, known to be widely distributed in southern Asia and Australasia, is newly recorded for Sulawesi Island. A key to the Sulawesian eusocial wasp species is provided. Their biogeographical characteristics are discussed to show that the Sulawesian eusocial wasp fauna is composed of Oriental elements.

Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests

Tropical mountain forests contribute disproportionately to terrestrial biodiversity but little is known about insect diversity in the canopy and how it is distributed between tree species. We sampled tree-specific arthropod communities from 28 trees by canopy fogging and analysed beetle communities which were first morphotyped and then identified by their DNA barcodes. Our results show that communities from forests at 1100 and 1700 m a.s.l. are almost completely distinct. Diversity was much lower in the upper forest while community structure changed from many rare, less abundant species to communities with a pronounced dominance structure. We also found significantly higher beta-diversity between trees at the lower than higher elevation forest where community similarity was high. Comparisons on tree species found at both elevations reinforced these results. There was little species overlap between sites indicating limited elevational ranges. Furthermore, we exploited the advantage of DNA barcodes to patterns of haplotype diversity in some of the commoner species. Our results support the advantage of fogging and DNA barcodes for community studies and underline the need for comprehensive research aimed at the preservation of these last remaining pristine forests.

A review of the Indonesian species of the family Signiphoridae (Hymenoptera, Chalcidoidea), with description of three new species

The Indonesian species of the family Signiphoridae (Hymenoptera, Chalcidoidea) are revised. Three species of Chartocerus are described as new (Chartocerus kartiniae Polaszek & Schmidt, sp. nov., C. sumatrensis Schmidt & Polaszek, sp. nov., and C. javensis Schmidt & Ubaidillah, sp. nov.) and four species of Signiphora, viz., S. bennetti Woolley & Dal Molin, S. flavella Girault, S. perpauca Girault and S. bifasciata Ashmead, are diagnosed.

DNA barcoding data release for Coleoptera from the Gunung Halimun canopy fogging workpackage of the Indonesian Biodiversity Information System (IndoBioSys) project

We present the results of a DNA barcoding pipeline that was established as part of the German-Indonesian IndobioSys project - Indonesian Biodiversity Information System. Our data release provides the first large-scale diversity assessment of Indonesian coleoptera obtained by canopy fogging. The project combined extensive fieldwork with databasing, DNA barcode based species delineation and the release of results in collaboration with Indonesian counterparts, aimed at supporting further analyses of the data. Canopy fogging on 28 trees was undertaken at two different sites, Cikaniki and Gunung Botol, in the south-eastern area of the Gunung Halimun-Salak National Park in West Java, Indonesia. In total, 7,447 specimens of Coleoptera were processed, of which 3,836 specimens produced DNA barcode sequences that were longer than 300 bp. A total of 3,750 specimens were assigned a Barcode Index Number (BIN), including 2,013 specimens from Cikaniki and 1,737 specimens from Gunung Botol. The 747 BINs, that were obtained, represented 39 families of Coleoptera. The distribution of specimens with BINs per tree was quite heterogeneous in both sites even in terms of the abundance of specimens or diversity of BINs. The specimen distribution per taxon was heterogeneous as well. Some 416 specimens could not be identified to family level, corresponding to 72 BINs that lack a family level identification. The data have shown a large heterogeneity in terms of abundance and distribution of BINs between sites, trees and families of Coleoptera. From the total of 747 BINs that were recovered, 421 (56%) are exclusive from a single tree. Although the two study sites were in close proximity and separated by a distance of only about five kilometres, the number of shared BINs between sites is low, with 81 of the 747 BINs. With this data release, we expect to shed some light on the largely hidden diversity in the canopy of tropical forests in Indonesia and elsewhere.

The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia

The Indonesian archipelago features an extraordinarily rich biota. However, the actual taxonomic inventory of the archipelago remains highly incomplete and there is hardly any significant taxonomic activity that utilises recent technological advances. The IndoBioSys project was established as a biodiversity information system aiming at, amongst other goals, creating inventories of the Indonesian entomofauna using DNA barcoding. Here, we release the first large scale assessment of the megadiverse insect groups that occur in the Mount Halimun-Salak National Park, one of the largest tropical rain-forest ecosystem in West Java, with a focus on Hymenoptera, Coleoptera, Diptera and Lepidoptera collected with Malaise traps. From September 2015 until April 2016, 34 Malaise traps were placed in different localities in the south-eastern part of the Halimun-Salak National Park. A total of 4,531 specimens were processed for DNA barcoding and in total, 2,382 individuals produced barcode compliant records, representing 1,195 exclusive BINs or putative species in 98 insect families. A total of 1,149 BINs were new to BOLD. Of 1,195 BINs detected, 804 BINs were singletons and more than 90% of the BINs incorporated less than five specimens. The astonishing heterogeneity of BINs, as high as 1.1 exclusive BIN per specimen of Diptera successfully processed, shows that the cost/benefit relationship of the discovery of new species in those areas is very low. In four genera of Chalcidoidea, a superfamily of the Hymenoptera, the number of discovered species was higher than the number of species known from Indonesia, suggesting that our samples contain many species that are new to science. Those numbers shows how fast molecular pipelines contribute substantially to the objective inventorying of the fauna giving us a good picture of how potentially diverse tropical areas might be.

Does colour matter? Genetic differentiation of colour morphs of the Asian golden web spider Nephila antipodiana (Araneae: Nephilidae)

Here we present the first attempt to test for genetic differentiation among four distinct colour morphs of the Asian golden web spider Nephila antipodiana Walckenaer. Fragments of the 18S rRNA (18S) and cytochrome c oxidase subunit I (COI) genes were sequenced in eight populations of N. antipodiana belonging to four distinct colour morphs: yellow, yellowish green, and two newly discovered morphs, reddish yellow and white-spotted. The nuclear sequences amplified from females of the four colour morphs were identical. The mitochondrial COI sequences, on the other hand, revealed slightly higher variation by recovering three haplotypes belonging to two different clades. Clade I comprises yellow, yellowish green and reddish yellow morphs from the mainland of Southeast Asia and Java, whereas clade II is restricted to white-spotted morph originating from Borneo. The low genetic divergence between both clades, despite being distinctive, undoubtedly provides new insight into the genetic diversity of this polymorphic species.

Similar alpha and beta diversity changes in tropical ant communities, comparing savannas and rainforests in Brazil and Indonesia

Local biodiversity can be expected to be similar worldwide if environmental conditions are similar. Here, we hypothesize that tropical ant communities with different types of regional species pools but at similar habitat types in Brazil and Indonesia show similar diversity patterns at multiple spatial scales, when comparing (1) the relative contribution of alpha and beta diversity to gamma diversity; (2) the number of distinct communities (community differentiation); and (3) the drivers of β-diversity (species replacement or species loss/gain) at each spatial scale. In both countries, rainforests and savannas (biome scale) were represented by three landscapes (landscape scale), each with four transects (site scale) and each transect with 10 pitfall traps (local scale). At the local scale, α-diversity was higher and β-diversity lower than expected from null models. Hence, we observed a high coexistence of species across biomes. The replacement of species seemed the most important factor for β-diversity among sites and among landscapes across biomes. Species sorting, landscape-moderated species distribution and neutral drift are potential mechanisms for the high β-diversity among sites within landscapes. At the biome scale, different evolutionary histories produced great differences in ant community composition, so the replacement of species is, at this scale, the most important driver of beta diversity. According to these key findings, we conclude that distinct regional ant species pools from similar tropical habitat types are similarly constrained across several spatial scales, regardless of the continent considered.

Biodiversity into your hands - A call for a virtual global natural history 'metacollection'

Background

Many scientific disciplines rely on correct taxon delineations and identifications. So does a great part of the general public as well as decision makers. Researchers, students and enthusiastic amateurs often feel frustrated because information about species remains scattered, difficult to access, or difficult to decipher. Together, this affects almost anyone who wishes to identify species or verify identifications. Many remedies have been proposed, but we argue that the role of natural history collections remains insufficiently appreciated. We suggest using state-of-the-art mass imaging technology and to join forces to create a global natural history metacollection on the internet, providing access to the morphology of tens of millions of specimens and making them available for automated digital image analysis.

Discussion

Robotic high-resolution imaging technology and fast (high performance) computer-based image stitching make it now feasible to digitize entire collection drawers typically used for arthropod collections, or trays or containers used for other objects. Resolutions of 500 megapixels and much higher are already utilized to capture the contents of 40x50 cm collection drawers, providing amazing detail of specimens. Flanked by metadata entry, this helps to create access to tens of thousands of specimens in days. By setting priorities and combining the holdings of the most comprehensive collections for certain taxa, drawer digitizing offers the unique opportunity to create a global, virtual metacollection.

The taxonomic and geographic coverage of such a collection could never be achieved by a single institution or individual. We argue that by joining forces, many new impulses will emerge for systematic biology, related fields and understanding of biodiversity in general.

Digitizing drawers containing unidentified, little-curated specimens is a contribution towards the beginning of a new era of online curation. It also will help taxonomists and curators to discover and process the millions of “gems” of undescribed species hidden in museum accessions.

Summary

Our proposal suggests creating virtual, high-resolution image resources that will, for the first time in history, provide access for expert scientists as well as students and the general public to the enormous wealth of the world’s natural history collections. We foresee that this will contribute to a better understanding, appreciation and increased use of biodiversity resources and the natural history collections serving this cause.

An extreme case of plant-insect codiversification: figs and fig-pollinating wasps

It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant-insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale cophylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on an average, wasps had sequences from 77% of 6 genes (5.6 kb), figs had sequences from 60% of 5 genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based cophylogenetic analyses further support the codiversification hypothesis. Biogeographic analyses indicate that the present-day distribution of fig and pollinator lineages is consistent with a Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant-insect interactions of coordinated dispersal and long-term codiversification. [Biogeography; coevolution; cospeciation; host switching; long-branch attraction; phylogeny.].

Phylogeny and evolution of life-history strategies in the Sycophaginae non-pollinating fig wasps (Hymenoptera, Chalcidoidea)

BACKGROUND

Non-pollinating Sycophaginae (Hymenoptera, Chalcidoidea) form small communities within Urostigma and Sycomorus fig trees. The species show differences in galling habits and exhibit apterous, winged or dimorphic males. The large gall inducers oviposit early in syconium development and lay few eggs; the small gall inducers lay more eggs soon after pollination; the ostiolar gall-inducers enter the syconium to oviposit and the cleptoparasites oviposit in galls induced by other fig wasps. The systematics of the group remains unclear and only one phylogeny based on limited sampling has been published to date. Here we present an expanded phylogeny for sycophagine fig wasps including about 1.5 times the number of described species. We sequenced mitochondrial and nuclear markers (4.2 kb) on 73 species and 145 individuals and conducted maximum likelihood and Bayesian phylogenetic analyses. We then used this phylogeny to reconstruct the evolution of Sycophaginae life-history strategies and test if the presence of winged males and small brood size may be correlated.

RESULTS

The resulting trees are well resolved and strongly supported. With the exception of Apocrytophagus, which is paraphyletic with respect to Sycophaga, all genera are monophyletic. The Sycophaginae are divided into three clades: (i) Eukoebelea; (ii) Pseudidarnes, Anidarnes and Conidarnes and (iii) Apocryptophagus, Sycophaga and Idarnes. The ancestral states for galling habits and male morphology remain ambiguous and our reconstructions show that the two traits are evolutionary labile.

CONCLUSIONS

The three main clades could be considered as tribes and we list some morphological characters that define them. The same biologies re-evolved several times independently, which make Sycophaginae an interesting model to test predictions on what factors will canalize the evolution of a particular biology. The ostiolar gall-inducers are the only monophyletic group. In 15 Myr, they evolved several morphological adaptations to enter the syconia that make them strongly divergent from their sister taxa. Sycophaginae appears to be another example where sexual selection on male mating opportunities favored winged males in species with small broods and wingless males in species with large broods. However, some species are exceptional in that they lay few eggs but exhibit apterous males, which we hypothesize could be due to other selective pressures selecting against the re-appearance of winged morphs.