Ecological changes have driven biotic exchanges across the Indian Ocean.

The Indian Ocean has a complex geological history that has drawn the attention of naturalists for almost a century now. Due to its tectonic history, many geological elements and processes have been evoked to explain the exchange of species between landmasses. Here, we revisited previous studies on twenty-three taxa to investigate trends across time since the Gondwana breakup. We investigated these datasets by applying a time-calibrated Bayesian framework to them and reconstructing their ancestral ranges. We conclude that ecological transformations have presented opportunities for the establishment of migrants. The role of donating and receiving migrants has shifted several times according to these transformations. Time-specific trends show weak evidence for the stepping-stones commonly suggested as physical routes between landmasses. However, before its collision with Asia, India may have served as an intermediary for such exchanges.

Taxonomy notes and new occurrence data of four species of atyid shrimp (Crustacea: Decapoda: Atyidae) in Vietnam, all described from China.

BACKGROUND: Freshwater shrimp of the family Atyidae De Haan, 1849 have been studied in Vietnam for more than a century. A total of 24 species of atyid shrimps from the genera Caridina H. Milne Edwards, 1837, Neocaridina Kubo, 1938, Atyopsis Chace, 1983 have been recorded from Vietnam. With 22 species, the majority are from the genus Caridina. In 2013, Karge and Klotz mentioned the occurrence of four yet undescribed species belonging to Paracaridina Liang, Guo & Tang, 1999 in Vietnam without taxonomic details.In general, studies of freshwater atyids in Vietnam are limited and most Vietnamese taxa await a taxonomic revision. The available data do not fully reflect their estimated species diversity in the country and distribution data are deficient. Here, we focus on four species of atyid shrimps from two genera, viz. Caridinacantonensis Yu, 1938, C.lanceifrons Yu, 1936, C.serrata Stimpson, 1860 and Neocaridinapalmata (Shen, 1948), all described from China and have been reported to occur in Vietnam. The previous reports on the occurrence of these species in Vietnam are largely unreliable due to taxonomic confusion. To contribute to the knowledge of these taxa, we provide the first verified distribution records of the four species in the country with some taxonomic remarks. NEW INFORMATION: This study shows the first taxonomically-verified distribution data of four atyid shrimp species originally described from China, but also reported from Vietnam, albeit under various species names and, in some cases, erroneously. These data allow the first meaningful discussion of the distribution in light of the reproductive strategy of these four species and, in conjunction with the taxonomic remarks, will contribute to the knowledge of these taxa. As a result of this research and data from previous studies, we now consider all four species as widespread and non-endemic, but land-locked (with a complete freshwater life cycle). In Vietnam, all four species are confined to the northern half of the country. Beyond Vietnam, we provide the first records for Caridinalanceifrons from southern Thailand, which suggests a major sampling gap in Indochina.

Lake Poso's shrimp fauna revisited: the description of five new species of the genus Caridina (Crustacea, Decapoda, Atyidae) more than doubles the number of endemic lacustrine species.

Lake Poso, an ancient lake system on the Indonesian island Sulawesi, harbours an endemic species flock of six, four lacustrine and two riverine species of the freshwater shrimp genus Caridina. In this study, five new lacustrine species are described, bringing the total to eleven species altogether. The number of lacustrine species is more than doubled to nine species compared to the last taxonomic revision in 2009. One of them, Caridina mayamareenae Klotz, Wowor & von Rintelen, sp. nov., even represents the first case of an atyid shrimp associated with freshwater snails which is morphologically adapted to living in shells. An integrative approach was used by providing a combination of morphological, ecological, and molecular data. Based on standard morphological characters, distribution, substrate preferences, and colouration of living specimens in the field, five distinct undescribed species could be distinguished. To support our species-hypothesis based on the mitochondrial genes 16S and COI, a molecular phylogeny was used for all eleven species from Lake Poso. All species form a well-supported monophyletic group, but only four morphospecies consistently correspond to mtDNA clades - a possible reason could be introgressive hybridisation, incomplete lineage sorting, or not yet fixed species boundaries. These results are discussed further in the context of adaptive radiation, which turned out to be more diverse than previously described. Finally, yet importantly, subjecting all new species to similar threats and to the same IUCN category and criterion than the previously described species from the lake is recommended.

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.

An annotated checklist and integrative biodiversity discovery of barnacles (Crustacea, Cirripedia) from the Moluccas, East Indonesia.

To contribute to the taxonomic knowledge of barnacles in this understudied area, the first checklist of barnacles from the Moluccas is presented, including additional information on morphology, distribution, and substrate as well as molecular data. The species of barnacles from the Moluccas have been determined using morphological analysis and DNA sequences. During 19 field trips conducted between January 2016 and September 2017, 1,513 specimens of 24 species of intertidal and one species of deep-sea barnacles were collected from 51 localities from the islands. Morphological and molecular analysis of the collected material detected members of three families of stalked barnacles and four families of acorn barnacles. In addition to sampling in the field, we also surveyed the literature on barnacles from the Moluccas. In total, our checklist comprises 97 species from the Moluccas including 23 new records, two of them yet to be described species. Results suggest that the Moluccas have a much higher diversity of barnacles than previously known, for example, from the reports of Challenger and Siboga expeditions. For further work, routine application of molecular systematics could aid the detection of cryptic species, while increased sampling of more islands and a taxonomic revision of several groups would likely lead to an even higher number of species than currently known.

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 complex evolutionary history and phylogeography of Caridina typus (Crustacea: Decapoda): long-distance dispersal and cryptic allopatric species.

The evolutionary history of the old, diverse freshwater shrimp genus Caridina is still poorly understood, despite its vast distribution - from Africa to Polynesia. Here, we used nuclear and mitochondrial DNA to infer the phylogeographic and evolutionary history of C. typus, which is one of only four species distributed across the entire range of the genus. Despite this species' potential for high levels of gene flow, questions have been raised regarding its phylogeographic structure and taxonomic status. We identified three distinct lineages that likely diverged in the Miocene. Molecular dating and ancestral range reconstructions are congruent with C. typus' early dispersal to Africa, possibly mediated by the Miocene Indian Ocean Equatorial Jet, followed by back dispersal to Australasia after the Jet's closure. Furthermore, several different species delimitation methods indicate each lineage represents a distinct (cryptic) species, contradicting current morphospecies delimitation of a single C. typus taxon. The evolutionary history of C. typus lineages is complex, in which ancient oceanic current systems and (currently unrecognised) speciation events preceded secondary sympatry of these cryptic species.

Three new species of Caridina (Decapoda: Atyidae) from Central Sulawesi and Buton Island, Indonesia, and a checklist of the islands' endemic species.

Three atyid shrimp species of the genus Caridina Milne Edwards, 1837, Caridina boehmei n. sp., C. laroeha and C. butonensis n. sp., are described from the Indonesian islands Sulawesi and Buton. Caridina boehinei n. sp. differs from its apparently next congener C. sulawesi Cai & Ng, 2009 by the shape of the spinulation of the male sexual appendages. Caridina laroeha resembles C. mahalona and C. opaensis, but can be distinguished by the length and armature of the rostrum, the length ratio of segments of the third maxilliped and the number of spinules on the uropodal diaeresis. Caridina butonensis n. sp. resembles to C. boehmei n. sp. and C. opaensis but can be distinguished by its peculiar truncated rostrum and by a more reduced podobranch on the second maxilliped.

Drawn to the dark side: a molecular phylogeny of freshwater shrimps (Crustacea: Decapoda: Caridea: Atyidae) reveals frequent cave invasions and challenges current taxonomic hypotheses.

Atyid freshwater shrimps are globally distributed and form an important part of freshwater ecosystems, particularly in the tropics and subtropics. Despite their widespread distribution and ecological importance, their phylogenetic relationships are largely unresolved. Here we present the first comprehensive molecular phylogeny of the Atyidae investigating the evolutionary relationships among 32 of the 42 genera using mitochondrial and nuclear markers. Our data indicate that the established classification of the Atyidae is in need of substantial taxonomic revision at all taxonomic levels. We suggest a new suprageneric systematization of atyids and discuss problematic issues at the generic level, particularly in the most speciose genus, Caridina. Molecular clock based divergence time estimates for atyids vary widely, but invariably support the assumption that atyids are an ancient freshwater lineage with an origin in the mid-Cretaceous at the very latest. Atyid distribution patterns are the result of instances of both long-distance dispersal and vicariance, depending largely on the reproductive mode of taxa. From an evolutionary perspective, the high frequency of independent origin of both a complete (landlocked) freshwater life cycle and a cave-dwelling mode of life is remarkable and unparalleled among crustaceans.

Adaptive radiation and ecological diversification of Sulawesi's ancient lake shrimps.

Ancient lakes are natural laboratories for the study of adaptive radiation. Recently, two lake systems on the Indonesian island Sulawesi have emerged as promising new model systems. A species flock of atyid freshwater shrimps in the Malili lake system comprises 15 colorful endemic taxa. Mitochondrial DNA data suggest two independent colonizations by riverine ancestors. Only one colonization event led to subsequent radiation into 14 species, while the second clade comprises just one species. The vast majority of species (n= 12) are habitat specialists, which are confined to the larger Malili clade and include all taxa with species-specific color patterns and a restricted distribution within the five connected Malili lakes. Morphological, genetic, and ecological data are consistent with the existence of an adaptive radiation in the Malili lakes, involving the habitat-specific diversification of trophic morphology. In addition to testing criteria for the recognition of an adaptive radiation, an ancestral state reconstruction reveals an equal probability for either a riverine generalist or a lacustrine specialist as ancestor of the large Malili clade, which is interpreted as indicative of an early stage of habitat specialization within this radiation. Finally, our results suggest that species diversification may have been primarily driven by ecological specialization and allopatric speciation.

Molecular phylogeny and diversification of freshwater shrimps (Decapoda, Atyidae, Caridina) from ancient Lake Poso (Sulawesi, Indonesia)--the importance of being colourful.

Ancient Lake Poso on the Indonesian island Sulawesi hosts a highly diverse endemic fauna, including a small species flock of atyid Caridina shrimps, which are characterized by conspicuous colour patterns. We used a mtDNA based molecular phylogeny to test the assumption of a monophyletic origin and intralacustrine radiation of the species flock and to assess the species specificity of some colour morphs. Our data reveal a rapid radiation of Caridina in the entire Poso drainage system, but provide no strong evidence for a monophyletic radiation of the lake species. Nevertheless each lacustrine species shows a varying degree of substrate or trophic specialization, usually considered a hallmark of adaptive radiation. Two distinct colour forms previously attributed to a single species, C. ensifera, lack distinguishing qualitative morphological characters, but are shown to be two different species. In contrast, morphologically rather distinct lake species lacking specific colour patterns may be hybridizing with riverine taxa. These results suggest that colour may play a similar role in species recognition and possibly speciation in ancient lake Caridina as hypothesized, e.g. for some African cichlids.

An island in the stream: Australia's place in the cosmopolitan world of Indo-West Pacific freshwater shrimp (Decapoda: Atyidae: Caridina).

Mitochondrial DNA sequences were used to investigate phylogenetic and biogeographic relationships among Australian freshwater shrimp from the genus Caridina H. Milne Edwards, 1837 (Atyidae) and congeners from potential source populations throughout the Indo-West Pacific region. Numerous Australian taxa have close evolutionary relationships with non-Australian taxa from locations throughout the region, indicating a diverse origin of the Australian freshwater fauna. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. Interestingly, a study on Australia's other main genus of atyid shrimp, Paratya Miers, 1882, inferred only a single colonisation. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater taxa, and so implies a vicariant explanation due to the development of colder, dryer climates during the late Miocene/early Pliocene.