Decadal comparison (1950–2020) of benthic marine flora from Central and Southern Vietnam

The benthic flora of Central and Southern Vietnam and its historical changes between 1950 and 2020 were studied. Three collections were compared: collection A (1950–1970), collection B (1980–2000) and collection С (2000–2020). In all collections (1950–2020), a total of 702 macroalgal taxa and their forms have been found, including 386 red (55%), 142 brown (20%) and 174 green (25%) algal taxa. A comparison of the collections has shown significant changes in species compositions of the marine flora during the period (the maximum similarity of the benthic flora of the three compared collections was about 63%). In each taxonomic group of macrophytes, there was a proportional replacement of some species by others. It is suggested that the revealed decadal changes in the marine flora of Central and Southern Vietnam are natural, periodic (seasonal, annual or perennial) and regulated by internal factors of the ecosystem.

Carboniferous fusuline Foraminifera: taxonomy, regional biostratigraphy, and palaeobiogeographic faunal development

This paper proposes a synthesis of the taxonomy, phylogeny, palaeogeographic distribution, regional biostratigraphy, and palaeobiogeographic faunal development of Carboniferous fusuline foraminifers. They appeared in the latest Tournaisian and comprised a small-sized, morphologically conservative taxonomic group during the Mississippian. Fusulines became larger and prevailed in Pennsylvanian foraminiferal assemblages. Carboniferous fusulines consist of Ozawainellidae, Staffellidae, Schubertellidae, Fusulinidae, and Schwagerinidae, in which 95 genera are considered as valid taxonomically. Upsizing their shells throughout the Pennsylvanian is likely related to symbiosis with photosynthetic microorganisms, which was accelerated by the acquisition of a keriothecal wall in Late Pennsylvanian schwagerinids. Regional fusuline succession data from 40 provinces provide a refined biostratigraphy, enabling zonation and correlation with substage- or higher-resolution precision in the Pennsylvanian. Their spatio-temporal faunal characteristics show that fusulines had a cosmopolitan palaeobiogeographic signature in Mississippian time, suggesting unrestricted faunal exchange through the palaeoequatorial Rheic Ocean. After the formation of Pangea, Pennsylvanian fusulines started to show provincialism, and their distributions defined the Ural-Arctic Region in the Boreal Realm, Palaeotethys, Panthalassa, and North American Craton regions in the Palaeoequatorial Realm, and Western Gondwana and Eastern Peri-Gondwana regions in the Gondwana Realm. The Western Palaeotethys and East European Platform Subregions maintained higher generic diversity throughout the Pennsylvanian.

Thailandina and Neothailandina and their family Thailandinidae salvaged: a valid taxonomic group of peculiar Permian fusuline Foraminifera

The fusuline genera Thailandina Toriyama and Kanmera, 1968 and Neothailandina Toriyama and Kanmera, 1968 were established by Toriyama and Kanmera (1968) based on material from the Khao Phlong Phrab section of the Permian Rat Buri Limestone in central Thailand that is currently assigned to the Khao Khad Formation of the Saraburi Group (Ueno and Charoentitirat, 2011). These fusuline genera are peculiar in having parachomata and replaced tests by secondary mineralization. Moreover, Neothailandina was described to have a test with transverse septula, considered to be characteristic for Neoschwagerinidae. Based on these remarkable test features, Toriyama and Kanmera (1968) newly introduced the subfamily Thailandininae to accommodate these two new genera and assigned it to the Neoschwagerinidae, despite the lack of septula in Thailandina. Later, Kobayashi et al. (2010) argued that Thailandina and Neothailandina are just a mixed grouping of several known genera of schwagerinids, verbeekinids, and neoschwagerinids that are too altered by recrystallization to be recognizable, and rejected the taxonomic validity of these two genera as well as Thailandininae. The Khao Phlong Phrab section represents one of the standard late Cisuralian−Guadalupian (late early−middle Permian) fusuline successions in the eastern Paleotethys (Zhang and Wang, 2018) and contains not only Thailandina and Neothailandina but also abundant schwagerinid, verbeekinid, and neoschwagerinid fusulines (Toriyama, 1975; Fig. 1). I investigated the original specimens described by Toriyama and Kanmera (1968) and Toriyama (1975) from the section that are housed in the Department of Earth and Planetary Sciences of Kyushu University, Japan. I found that most of the grounds for Kobayashi et al.'s (2010) arguments to regard the thailandinin genera as taxonomically invalid are not supported by observations on these specimens as explained in the account that follows. In this taxonomic note, I propose that Thailandina and Neothailandina, and their family Thailandinidae, should be retained as valid taxonomic groups.

Phagotrophic protists (protozoa) in Antarctic terrestrial ecosystems: diversity, distribution, ecology, and best research practices

Phagotrophic protists (formerly protozoa) are a highly diverse, polyphyletic grouping of generally unicellular, heterotrophic eukaryotes that are key regulators of the soil microbiome. The biodiversity and ecology of soil phagotrophic protists are still largely uncharacterized, especially in the Antarctic, which possesses some of the harshest terrestrial environments known and potentially many physiologically unique and scientifically interesting species. Antarctic soil systems are also highly limited in terms of moisture, temperature, and carbon, and the resulting reduced biological complexity can facilitate fine-tuned investigation of the drivers and functioning of microbial communities. To facilitate and encourage future research into protist biodiversity and ecology, especially in context of the broader functioning of Antarctic terrestrial communities, I review the biodiversity, distribution, and ecology of Antarctic soil phagotrophic protists. Biodiversity appears to be highly structured by region and taxonomic group, with the Antarctic Peninsula having the highest taxonomic diversity and ciliates (Ciliophora) being the most diverse taxonomic group. However, richness estimates are likely skewed by disproportionate sampling (over half of the studies are from the peninsula), habitat type bias (predominately moss-associated soils), investigator bias (toward ciliates and the testate amoeba morphogroup), and methodological approach (toward cultivation and morphological identification). To remedy these biases, a standardized methodology using both morphological and molecular identification and increased emphasis on microflagellate and naked amoeba morphogroups is needed. Additionally, future research should transition away from biodiversity survey studies to dedicated ecological studies that emphasize the function, ecophysiology, endemicity, dispersal, and impact of abiotic drivers beyond moisture and temperature.

15 years of introgression studies: quantifying gene flow across Eukaryotes

With the rise of affordable next generation sequencing technology, introgression - or the exchange of genetic materials between taxa - is widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment on the frequency of introgression in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by providing a meta-analysis of the most comprehensive survey of introgression studies in Eukaryotes to date (724 papers with claims of introgression). We first examined the evidence given to support introgression, and if/how the lines of evidence have changed across time. We then collated a single statistic, Patterson's D, that quantifies the strength of introgression across 123 studies to further assess how taxonomic group, divergence time, and aspects of life history influence introgression. We find three main results. Studies on introgression are much more frequent in plants and mammals than any other taxonomic group. The study of introgression has shifted from a largely qualitative assessment of whether introgression happens, to a focus on when and how much introgression has occurred across taxa. The most-often used introgression statistic, Patterson's D, shows several intriguing patterns suggesting introgression reports may be biased by both differences in reporting criteria and sequencing technology, but may also differ across taxonomic systems and throughout the process of speciation. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities, and highlight important areas of future research that can be better assessed once this unified approach is met.

Papers and New Species of Minor Insect Orders Published in Zootaxa, 2001–2020

A summary is presented of papers published on minor insect orders (MIO) in Zootaxa’s first 20 years, as well as the number of new species described therein. The MIO orders currently covered by the editors and summarized here include Archaeognatha (Microcoryphia), Dermaptera, Embioptera, Siphonaptera, Zoraptera and Zygentoma, as well as the hexapod classes Protura and Diplura. Both fossil and extant taxa of these groups are included in the MIO purview. The MIO editors also have frequently served as interim editors for groups temporarily without a subject-matter editor, such as Carabidae, Blattodea and Mantodea; as a backup editor for Mecoptera; and as ad-hoc editors for papers written by the editors of a different taxonomic group or for papers without a single-taxon focus. In the period 2001‒2020, descriptions of 130 new species were published, compared with 816 species in all other journals. The greatest number of species were for Protura (49), while Zoraptera had the highest proportion of papers compared to all publications (50%).

PlantRep: a resource of plant repeats

We re-annotated repeats sequence of 459 plant genomes and release a new resource of plant repeats: PlantRep (http://www.plantrep.cn/). We compared the structural and evolutionary characteristics of repeat sequences in different plant taxonomic group. The contribution of repeat sequences to the genes was examined systematically. PlantRep sheds lights of evolution of plant repeats and provides a free-resource for deep annotation of genome and comparative genomics research of repeat elements in plants.