A New Integrated Approach to Taxonomy: The Fusion of Molecular and Morphological Systematics with Type Material in Benthic Foraminifera

Cenozoic climatic changes drive evolution and dispersal of coastal benthic foraminifera in the Southern Ocean

The Antarctic coastal fauna is characterized by high endemism related to the progressive cooling of Antarctic waters and their isolation by the Antarctic Circumpolar Current. The origin of the Antarctic coastal fauna could involve either colonization from adjoining deep-sea areas or migration through the Drake Passage from sub-Antarctic areas. Here, we tested these hypotheses by comparing the morphology and genetics of benthic foraminifera collected from Antarctica, sub-Antarctic coastal settings in South Georgia, the Falkland Islands and Patagonian fjords. We analyzed four genera (Cassidulina, Globocassidulina, Cassidulinoides, Ehrenbergina) of the family Cassidulinidae that are represented by at least nine species in our samples. Focusing on the genera Globocassidulina and Cassidulinoides, our results showed that the first split between sub-Antarctic and Antarctic lineages took place during the mid-Miocene climate reorganization, probably about 20 to 17 million years ago (Ma). It was followed by a divergence between Antarctic species ~ 10 Ma, probably related to the cooling of deep water and vertical structuring of the water-column, as well as broadening and deepening of the continental shelf. The gene flow across the Drake Passage, as well as between South America and South Georgia, seems to have occurred from the Late Miocene to the Early Pliocene. It appears that climate warming during 7-5 Ma and the migration of the Polar Front breached biogeographic barriers and facilitated inter-species hybridization. The latest radiation coincided with glacial intensification (~ 2 Ma), which accelerated geographic fragmentation of populations, demographic changes, and genetic diversification in Antarctic species. Our results show that the evolution of Antarctic and sub-Antarctic coastal benthic foraminifera was linked to the tectonic and climatic history of the area, but their evolutionary response was not uniform and reflected species-specific ecological adaptations that influenced the dispersal patterns and biogeography of each species in different ways.

New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

Recent years have brought undeniable progress in tardigrade taxonomy, and speciose complexes were detected in a number of phylogenetic lineages. The family Echiniscidae is one such lineage; it is one of the most diverse groups of limno-terrestrial tardigrades and can be characterized as having achieved great evolutionary success. In this contribution, using populations representing several species that originated from the Indomalayan region, we reconstructed phylogenetic affinities within Nebularmis, a recently erected genus within the Echiniscus lineage. Nebularmis auratus sp. nov. and Nebularmis burmensis sp. nov. are described from the Eastern Yoma Mountains and the Shan Hills (Myanmar), Nebularmis bhutanensis sp. nov. is described from the Eastern Himalayas (Bhutan), and Nebularmis indicus sp. nov. is described from the foothills of the Western Ghats (Goa, India). Moreover, males are reported in populations of the last two species. All known members of the genus can be phenotypically differentiated based on minute details of their dorsal sculpture and claws. Moreover, a very wide tropical distribution is demonstrated for Nebularmis cirinoi, recorded for the first time from islands of the Malay Archipelago. Furthemore, novel morphological, genetic, and geographic data allowed for the clarification of the generic diagnosis. Currently available data favor a scenario under which Nebularmis evolved in Southeast Asia and later dispersed to other regions of the globe.

Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia

Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.

Response of a kleptoplastidic foraminifer to heterotrophic starvation: photosynthesis and lipid droplet biogenesis

The aim of this work is to document the complex nutritional strategy developed by kleptoplastic intertidal foraminifera. We study the mixotrophic ability of a common intertidal foraminifer, Elphidium williamsoni, by (i) investigating the phylogenetic identity of the foraminiferal kleptoplasts, (ii) following their oxygenic photosynthetic capacity and (iii) observing the modification in cellular ultrastructural features in response to photoautotrophic conditions. This was achieved by coupling molecular phylogenetic analyses and TEM observations with non-destructive measurements of kleptoplast O2 production over a 15-day experimental study. Results show that the studied E. williamsoni actively selected kleptoplasts mainly from pennate diatoms and had the ability to produce oxygen, up to 13.4 nmol O2 cell-1 d-1, from low to relatively high irradiance over at least 15 days. Ultrastructural features and photophysiological data showed significant differences over time, the number of lipid droplets, residual bodies and the dark respiration increased; whereas, the number of kleptoplasts decreased accompanied by a minor decrease of the photosynthetic rate. These observations suggest that in E. williamsoni kleptoplasts might provide extra carbon storage through lipid droplets synthesis and highlight the complexity of E. williamsoni feeding strategy and the necessity of further dedicated studies regarding mechanisms developed by kleptoplastidic foraminifera for carbon partitioning and storage.

Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera

Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene. Living foraminiferal specimens were collected from two intertidal mudflats of the Wadden Sea and DNA was extracted from foraminiferal individuals and from the surrounding sediments. Molecular analysis allowed us to confirm that our foraminiferal specimens belong to three genetic types: Ammonia sp. T6, Elphidium sp. S5 and Haynesina sp. S16. Foraminiferal intracellular eukaryote communities reflected to an extent those of the surrounding sediments but at different relative abundances. Unlike sediment eukaryote communities, which were largely determined by the sampling site, foraminiferal intracellular eukaryote communities were driven by foraminiferal species, followed by sediment depth. Our data suggests that Ammonia sp. T6 can predate on metazoan classes, whereas Elphidium sp. S5 and Haynesina sp. S16 are more likely to ingest diatoms. These observations, alongside the use of metabarcoding in similar ecological studies, significantly contribute to our overall understanding of the ecological roles of these protists in intertidal benthic environments and their position and function in the benthic food webs.

Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species

The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang & Chen, sp. nov.; Pseudostegana amnicola Zhang & Chen, sp. nov.; Pseudostegana amoena Zhang & Chen, sp. nov.; Pseudostegana mailangang Zhang & Chen, sp. nov.; Pseudostegana meiduo Zhang & Chen, sp. nov.; Pseudostegana meiji Zhang & Chen, sp. nov.; Pseudostegana mystica Zhang & Chen, sp. nov.; Pseudostegana stictiptrata Zhang & Chen, sp. nov.; Pseudostegana stigmatptera Zhang & Chen, sp. nov.; Pseudostegana ximalaya Zhang & Chen, sp. nov. and Pseudostegana zhuoma Zhang & Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different.