Taxonomic Uncertainty Research Articles

Molecular differentiation of the Murraya paniculata Complex (Rutaceae: Aurantioideae: Aurantieae)

BackgroundOrange jasmine has a complex nomenclatural history and is now known as Murraya paniculata (L.) Jack. Our interest in this common ornamental stemmed from the need to resolve its identity and the identities of closely related taxa as hosts of the pathogen ‘Candidatus Liberibacter asiaticus’ and its vector Diaphorina citri. Understanding these microbe-vector-plant relationships has been hampered by taxonomic confusion surrounding Murraya at both the generic and specific levels.ResultsTo resolve the taxonomic uncertainty, six regions of the maternally-inherited chloroplastal genome and part of the nuclear-encoded ITS region were amplified from 85 accessions of Murraya and Merrillia using the polymerase chain reaction (PCR). Clustering used maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI). Chronograms were produced for molecular dating, and to test the monophyly of Murraya rigorously, using selected accessions of Murraya and 26 accessions of the Rutaceae and Simarubaceae. Sequence data from the ITS and chloroplastal regions suggest that Murraya paniculata (sensu (Swingle WT and Reece CR, The Citrus Industry, p. 190–430, 1967)) can be separated into four distinct but morphologically somewhat cryptic taxa: Murraya paniculata (sensu (Mabberley DJ, Taxon 65:366–371, 2016)), M. elongata, M. sumatrana and M. lucida. In addition, Murraya omphalocarpa was identified as a putative hybrid of M. paniculata and M. lucida with two geographically isolated nothovarieties representing reciprocal crosses. Murraya is monophyletic, and molecular dating suggests that it diverged from Merrillia during the Miocene (23–5 Ma) with this Murraya group speciating and dispersing during the Middle Miocene onwards.ConclusionsThe accessions from Asia and Australasia used in this study grouped into biogeographical regions that match herbarium specimen records for the taxa that suggest natural allopatric distributions with limited overlap and hybridity. Murraya paniculata has been distributed around the world as an ornamental plant. The division of the Murraya paniculata complex into four species with a rare hybrid also confirms morphological studies.

Species delimitation based on integrative approach suggests reallocation of genus in Hypostomini catfish (Siluriformes, Loricariidae)

Integrative approaches are particularly useful to resolve taxonomic uncertainties in species-rich groups that have undergone explosive radiation, such as Hypostomini (suckermouth armored catfishes). This tribe encompasses the genera Hypostomus and Pterygoplichthys, but the actual number of species in each genus and the intergeneric interrelationships are confusing or unknown for some ecoregions in the Neotropics. Here, we analyzed three endemic species Hypostomus chrysostiktos, H. jaguar and H. unae from Northeastern Mata Atlântica in northeastern Brazil based on meristic characters, geometric morphometrics, chromosomal data, DNA barcode and species delimitation algorithms. The current taxonomic status of these catfishes is challenged. While H. unae and H. jaguar revealed a close evolutionary relationship similar to those observed within Hypostomus from other basins, H. chrysostiktos was herein more closely related to Pterygoplichthys, being invariably recovered as a highly distinctive taxonomic unit than to Hypostomus. Therefore, we recommend the reallocation of H. chrysostiktos as Pterygoplichthys chrysostiktos and a thorough systematic review of Pterygoplichthys, particularly focusing on putative convergence traits in relation to Hypostomus.

DNA barcoding of fruit flies (Diptera: Tephritidae) in Thailand: ambiguity, misidentification and cryptic diversity

Fruit flies (Diptera: Tephritidae) are significant insect pests of many commercially important fruits and vegetables. Therefore, rapid and accurate species identification methods are required for the regulation, management and quarantine of these pests. In this study, we examined the efficiency of mitochondrial cytochrome c oxidase I sequences for species identification of fruit flies in Thailand. Data analyses based on 42 fruit fly taxa revealed moderate performance of this genetic marker. There were 14 taxa that have no barcode gap and thus could not be identified unambiguously to species by this methodology. Taxonomic uncertainty, inadequate variation of the marker and misidentifications of specimens deposited in the public database are the most likely factors explaining unsuccessful identification. DNA barcodes also revealed cryptic diversity in five taxa (Bactrocera caudata, B. tuberculata, B. infesta, Zeugodacus isolatus, Carpomya vesuviana). These species require further taxonomic investigation of if they are different cryptic taxa or are indications of geographic structuring of within single species.

Description of three new velvet geckos (Diplodactylidae: Oedura) from inland eastern Australia, and redescription of Oedura monilis De Vis.

Inland eastern Australia has a complex array of habitats, driven by variation in topography, geology and moisture. This broad region is relatively poorly surveyed compared to coastal eastern Australia and likely contains significant numbers of undescribed reptiles. Oedura monilis is found through much of this region but has been shrouded in taxonomic uncertainty since its original description. Here I assess variation across the range of 'O. monilis' and show that it consists of two species: a widespread species in the northern half of the range and a widespread species in the southern half of the range. These two species are readily diagnosed by colour pattern and aspects of shape and scalation. I show that the name O. monilis applies to the northern species. I also show that the name O. attenboroughi Wells Wellington applies to the northern populations, making it a junior synonym of O. monilis. I describe the southern widespread species as Oedura elegans sp. nov.. I also describe two new, highly localised species from inland eastern Queensland that are allied to O. monilis: Oedura picta sp. nov. from a rocky range in the Moranbah-Dysart region, and Oedura lineata sp. nov. from brigalow forest remnants in the Arcadia Valley. These two species are distinct for colour pattern and aspects of size, shape and scalation. Oedura lineata sp. nov. has a very small and fragmented range, and is restricted to a highly threatened habitat type. It therefore warrants conservation attention. I also provide more detailed diagnoses for O. coggeri Bustard and O. tryoni De Vis, and demonstrate that the name O. ocellata Boulenger is a junior synonym of O. tryoni.

Accounting for uncertainty in assessing the impact of climate change on biodiversity hotspots in Spain

Our limited understanding of the complexity of nature generates uncertainty in mathematical and cartographical models used to predict the effects of climate change on species’ distributions. We developed predictive models of distributional range shifts of threatened vertebrate species in mainland Spain, and in their accumulation in biodiversity hotspots due to climate change. We considered two relevant sources of climatological uncertainty that affect predictions of future climate: general circulation models and socio–economic scenarios. We also examined the relative importance of climate as a driver of species’ distribution and taxonomic uncertainty as additional biogeographical causes of uncertainty. Uncertainty was detected in all the forecasts derived from models in which climate was a significant explanatory factor, and in the species with taxonomic uncertainty. Uncertainty in forecasts was mainly located in areas not occupied by the species, and increased with time difference from the present. Mapping this uncertainty allowed us to assess the consistency of predictions regarding future changes in the distribution of hotspots of threatened vertebrates in Spain.

Heat‐induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea

The coral holobiont is a complex ecosystem consisting of coral animals and a highly diverse consortium of associated microorganisms including algae, fungi, and bacteria. Several studies have highlighted the importance of coral‐associated bacteria and their potential roles in promoting the host fitness and survival. Recently, dynamics of coral‐associated microbiomes have been demonstrated to be linked to patterns of coral heat tolerance. Here, we examined the effect of elevated seawater temperature on the structure and diversity of bacterial populations associated with Porites lutea, using full‐length 16S rRNA sequences obtained from Pacific Biosciences circular consensus sequencing. We observed a significant increase in alpha diversity indices and a distinct shift in microbiome composition during thermal stress. There was a marked decline in the apparent relative abundance of Gammaproteobacteria family Endozoicomonadaceae after P. lutea had been exposed to elevated seawater temperature. Concomitantly, the bacterial community structure shifted toward the predominance of Alphaproteobacteria family Rhodobacteraceae. Interestingly, we did not observe an increase in relative abundance of Vibrio‐related sequences in our heat‐stressed samples even though the appearance of Vibrio spp. has often been detected in parallel with the increase in the relative abundance of Rhodobacteraceae during thermal bleaching in other coral species. The ability of full‐length 16S rRNA sequences in resolving taxonomic uncertainty of associated bacteria at a species level enabled us to identify 24 robust indicator bacterial species for thermally stressed corals. It is worth noting that the majority of those indicator species were members of the family Rhodobacteraceae. The comparison of bacterial community structure and diversity between corals in ambient water temperature and thermally stressed corals may provide a better understanding on how bacteria symbionts contribute to the resilience of their coral hosts to ocean warming.

Morphological plasticity in a Fijian Seagrass: Halophila ovalis subsp. bullosa

Seagrasses are marine flowering plants found along both tropical and temperate coastlines; they possess great ecological importance as nurseries, nutrient sinks, and providers of critical marine habitat. Understanding the distribution and diversity of seagrass habitats is important for their conservation and management, however this is impeded by varying species’ diversity, the extensive distribution of seagrasses and taxonomic uncertainty. In the Fiji Islands, the tropical seagrass Halophila ovalis and its subspecies H. ovalis bullosa are the subject of taxonomic controversy, as a singular morphological characteristic distinguishes the two. This characteristic is the bullated, or blister-like leaves of the latter, compared to the smooth leaves of the former, which in some instances have been observed on the same plant (S.S., pers. obs.). This study examined material from both taxa, along with three other seagrass species (Halodule pinifolia, H. uninervis and Syringodium isoetifolium; total n=95) and used independent morphological and molecular barcoding approaches to assess the conspecificity of the two Halophila taxa. Examination of vegetative and reproductive characters was not able to distinguish between H. ovalis and H. ovalis subsp. bullosa, while phylogenetic reconstructions using ITS2, matK and trnH-psbA barcodes supported their monophyly. We recommend revision and merger of these taxa, while the approach used here is highly useful for taxonomic resolution in other seagrass taxa, for their conservation, restoration and management.

Species complexes and the importance of Data Deficient classification in Red List assessments: The case of Hylobatrachus frogs

Taxonomy is the cornerstone of extinction risk assessments. Currently, the IUCN Red List treats species complexes either under a single overarching species name—resulting in an unhelpfully broad circumscription and underestimated threat assessment that does not apply to any one species lineage—or omits them altogether—resulting in the omission of species that should be assessed. We argue that taxonomic uncertainty alone, as in species complexes, should be grounds for assessment as Data Deficient (DD). Yet, use of the DD category is currently discouraged, resulting in assessments based on poor data quality and dismissal of the importance of taxonomic confidence in conservation. This policy may be leading to volatile and unwarranted assessments of hundreds of species across the world, and needs to be revised. To illustrate this point, we here present a partial taxonomic revision of torrent frogs from eastern Madagascar in the Mantidactylus subgenus Hylobatrachus. Two named species, Mantidactylus (Hylobatrachus) lugubris and M. (H.) cowanii, and several undescribed candidate species are recognised, but the application of the available names has been somewhat ambiguous. In a recent re-assessment of its conservation status, M. (H.) lugubris was assessed including all complex members except M. (H.) cowanii within its distribution, giving it a status of Least Concern and distribution over most of eastern Madagascar. After describing two of the unnamed lineages as Mantidactylus (Hylobatrachus) atsimo sp. nov. (from southeastern Madagascar) and Mantidactylus (Hylobatrachus) petakorona sp. nov. (from the Marojejy Massif in northeastern Madagascar), we show that Mantidactylus (Hylobatrachus) lugubris is restricted to the central east of Madagascar, highlighting the inaccuracy of its current Red List assessment. We propose to re-assess its status under a more restrictive definition that omits well-defined candidate species, thus representing the actual species to which its assessment refers, to the best of current knowledge. We recommend that for species complexes in general, (1) nominal lineages that can be confidently restricted should be assessed under the strict definition, (2) non-nominal species-level lineages and ambiguous names should be prioritised for taxonomic research, and (3) ambiguous names should be assessed as DD to highlight the deficiency in data on their taxonomic status, which is an impediment to their conservation. This would reduce ambiguity and underestimation of threats involved in assessing species complexes, and place the appropriate emphasis on the importance of taxonomy in anchoring conservation.

High-Resolution Profiling of Gut Bacterial Communities in an Invasive Beetle using PacBio SMRT Sequencing System

Dendroctonus valens, an invasive bark beetle, has caused severe damage to Chinese forests. Previous studies have highlighted the importance of the gut microbiota and its fundamental role in host fitness. Culture-dependent and culture-independent methods have been applied in analyzing beetles’ gut microbiota. The former method cannot present a whole picture of the community, and the latter mostly generates short read lengths that cannot be assigned to species. Here, the PacBio sequencing system was utilized to capture full-length 16S rRNA sequences in D. valens gut throughout its ontogeny. A total of eight phyla, 55 families, 102 genera, and 253 species were identified. Bacterial communities in colonized beetles have the greatest richness but the lowest evenness in all life stages, which is different from those in young larvae. Pseudomonas sp., Serratia liquefaciens possess high abundance throughout its ontogeny and may serve as members of the core bacteriome. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis predicted that gut microbiota in larvae are rich in genes involved in carbohydrate, energy metabolism. Gut microbiota in both larvae and colonized beetles are rich in xenobiotics and terpenoids biodegradation, which are decreased in dispersal beetles. Considering that the results are based mainly on the analysis of 16S rRNA sequencing and PICRUSt prediction, further confirmation is needed to improve the knowledge of the gut microbiota in D. valens and help to resolve taxonomic uncertainty at the species level.

Homoplasy or plesiomorphy? Reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata

Recent mitogenomic studies have exposed a gene order (GO) shared by two classes, four orders and 31 species (‘common GO’) within the flatworm subphylum Neodermata. There are two possible hypotheses for this phenomenon: convergent evolution (homoplasy) or shared ancestry (plesiomorphy). To test those, we conducted a meta-analysis on all available mitogenomes to infer the evolutionary history of GO in Neodermata. To improve the resolution, we added a newly sequenced mitogenome that exhibited the common GO, Euryhaliotrema johni (Ancyrocephalinae), to the dataset. Phylogenetic analyses conducted on two datasets (nucleotides of all 36 genes and amino acid sequences of 12 protein coding genes) and four algorithms (MrBayes, RAxML, IQ-TREE and PhyloBayes) produced topology instability towards the tips, so ancestral GO reconstructions were conducted using TreeREx and MLGO programs using all eight obtained topologies, plus three unique topologies from previous studies. The results consistently supported the second hypothesis, resolving the common GO as a plesiomorphic ancestral GO for Neodermata, Cestoda, Monopisthocotylea, Cestoda + Trematoda and Cestoda + Trematoda + Monopisthocotylea. This allowed us to trace the evolutionary GO scenarios from each common ancestor to its descendants amongst the Monogenea and Cestoda classes, and propose that the common GO was most likely retained throughout all of the common ancestors, leading to the extant species possessing the common GO. Neodermatan phylogeny inferred from GOs was largely incongruent with all 11 topologies described above, but it did support the mitogenomic dataset in resolving Polyopisthocotylea as the earliest neodermatan branch. Although highly derived GOs might be of some use in resolving isolated taxonomic and phylogenetic uncertainties, we conclude that, due to the discontinuous nature of their evolution, they tend to produce artefactual phylogenetic relationships, which makes them unsuitable for phylogenetic reconstruction in Neodermata. Wider and denser sampling of neodermatan mitogenomic sequences will be needed to infer the evolutionary pathways leading to the observed diversity of GOs with confidence.

The complete chloroplast genome sequence of Dactylorhiza majalis (Rchb.) P.F. Hunt et Summerh. (Orchidaceae)

The complete chloroplast genome of Dactylorhiza majalis (Rchb.) P.F. Hunt et Summerh. (Orchidaceae:Orchidoideae) was assembled and characterized using next-generation sequencing data. The plastome (154,108 bp) possesses the typical circular structure consisting of a large single-copy region (LSC; 83,196 bp), a small single-copy region (SSC; 26,580 bp), and two copies of inverted repeats (17,752 bp each). Its overall GC content is 36.99% and the plastome encodes 134 genes. Reconstruction of phylogenetic relationships using complete plastome sequences of Orchidaceae representatives showed that D. majalis was nested within the Orchidoideae tribe Orchideae. The complete plastome comprises a valuable tool in elucidating taxonomic uncertainties within the genus Dactylorhiza.

Building a DNA barcode library for the freshwater fishes of Bangladesh

We sequenced the standard DNA barcode gene fragment in 694 newly collected specimens, representing 243 species level Operational Barcode Units (OBUs) of freshwater fishes from Bangladesh. We produced coi sequences for 149 out of the 237 species already recorded from Bangladesh. Another 83 species sequenced were not previously recorded for the country, and include about 30 undescribed or potentially undescribed species. Several of the taxa that we could not sample represent erroneous records for the country, or sporadic occurrences. Species identifications were classified at confidence levels 1(best) to 3 (worst). We propose the new term Operational Barcode Unit (OBU) to simplify references to would-be DNA barcode sequences and sequence clusters. We found one case where there were two mitochondrial lineages present in the same species, several cases of cryptic species, one case of introgression, one species yielding a pseudogene to standard barcoding primers, and several cases of taxonomic uncertainty and need for taxonomic revision. Large scale national level DNA barcode prospecting in high diversity regions may suffer from lack of taxonomic expertise that cripples the result. Consequently, DNA barcoding should be performed in the context of taxonomic revision, and have a defined, competent end-user.

A population genetic assessment of taxonomic species: The case of Lake Malawi cichlid fishes.

Organisms sampled for population‐level research are typically assigned to species by morphological criteria. However, if those criteria are limited to one sex or life stage, or the organisms come from a complex of closely related forms, the species assignments may misdirect analyses. The impact of such sampling can be assessed from the correspondence of genetic clusters, identified only from patterns of genetic variation, to the species identified using only phenotypic criteria. We undertook this protocol with the rock‐dwelling mbuna cichlids of Lake Malawi, for which species within genera are usually identified using adult male coloration patterns. Given high local endemism of male colour patterns, and considerable allele sharing among species, there persists considerable taxonomic uncertainty in these fishes. Over 700 individuals from a single transect were photographed, genotyped and separately assigned: (a) to morphospecies using photographs; and (b) to genetic clusters using five widely used methods. Overall, the correspondence between clustering methods was strong for larger clusters, but methods varied widely in estimated number of clusters. The correspondence between morphospecies and genetic clusters was also strong for larger clusters, as well as some smaller clusters for some methods. These analyses generally affirm (a) adult male‐limited sampling and (b) the taxonomic status of Lake Malawi mbuna, as the species in our study largely appear to be well‐demarcated genetic entities. More generally, our analyses highlight the challenges for clustering methods when the number of populations is unknown, especially in cases of highly uneven sample sizes.

Extensive regional endemism and cryptic diversity in the Tennessee and Kentucky, USA populations of the burrowing crayfish Cambarus deweesae (Bouchard & Etnier, 1979) (Decapoda: Astacidea: Cambaridae) as revealed by molecular genetics

Abstract The southeastern United States is a global hotspot for crayfish biodiversity, with more than 300 described species in the region. Some of this diversity is unfortunately being threatened by anthropogenic activities and nearly one fifth of the North American crayfish species are currently threatened with extinction. Efforts to protect crayfish species have been hindered by a lack of information regarding their taxonomy, distribution, and conservation status. Here we target populations of the burrowing valley flame crayfish, Cambarus deweesae (Bouchard & Etnier 1979) for molecular taxonomy investigation. This species was originally known from the Clinch and Emory subdrainages in eastern Tennessee but it is currently listed as state endangered. The reporting of additional populations in Tennessee and Kentucky, however, has led to uncertainty about its conservation status. We analyzed sequence data from three mitochondrial genes (COI, 12S rRNA, and 16S rRNA) and from one nuclear gene (GAPDH) to decipher taxonomic questions regarding 15 crayfish populations, including 13 populations that are morphologically similar to C. deweesae (type locality sensu stricto). Combined analysis of all four genes demonstrated reciprocal monophyly for 14 out of 15 populations surveyed. Species delimitation methods, including GMYC and ABGD, identified between 11 and 13 new distinct genetic entities based on sequence divergence at the mitochondrial COI gene. Molecular results are combined with information on morphology and distribution in order to resolve taxonomic uncertainties within C. deweesae and its close relatives. The study highlights the need for fine-scale investigations into the phylogeography of North American burrowing crayfishes.

Oceanographic barriers, divergence, and admixture: Phylogeography and taxonomy of two putative subspecies of short-finned pilot whale.

Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short-finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the "Naisa" and "Shiho" forms. Using samples (n=735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short-finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short-finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally-distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.

Cycad forensics: leaflet micromorphology as a taxonomic tool for South African cycads

Cycads, a primitive group of gymnosperms, are currently facing extinction in many parts of the world. In South Africa, this is largely attributed to the illegal poaching of many threatened species. In the illegal trade of cycads, many highly threatened species are often deliberately misnamed as a more common species. Due to macromorphological similarity between many Encephalartos species, as well as taxonomic uncertainties that exist, species identification is also problematic. This study compared the utility of selected leaflet micromorphological characters as a taxonomic tool to independently identify eight South African cycad species. The characters, which included trichome type (if present), stomatal density and dimensions, stomatal band width and vein band width, were compared within four pairs of macromorphologically similar species. Quantitative and qualitative data on the characters were collected using stereomicroscopy, scanning electron microscopy (SEM) and variable pressure SEM. Results indicated that the majority of these characters varied significantly (p < 0.05) between paired species. Importantly, the presence of trichomes on mature leaflets of four species appears to be previously unreported. Trichome type, stomatal width and band width, and vein band width were identified as diagnostic characters that may be used to distinguish between species. The results validate the use of leaflet micromorphological characters, particularly stomatal and vein band widths (given the ease with which they can be measured), for distinguishing between macromorphologically similar cycad species.

Taxonomy and conservation of grassland earless dragons: new species and an assessment of the first possible extinction of a reptile on mainland Australia.

Taxonomic research is of fundamental importance in conservation management of threatened species, providing an understanding of species diversity on which management plans are based. The grassland earless dragon lizards (Agamidae: Tympanocryptis) of southeastern Australia have long been of conservation concern but there have been ongoing taxonomic uncertainties. We provide a comprehensive taxonomic review of this group, integrating multiple lines of evidence, including phylogeography (mtDNA), phylogenomics (SNPs), external morphology and micro X-ray CT scans. Based on these data we assign the lectotype of T. lineata to the Canberra region, restrict the distribution of T. pinguicolla to Victoria and name two new species: T. osbornei sp. nov. (Cooma) and T. mccartneyi sp. nov. (Bathurst). Our results have significant conservation implications. Of particular concern is T. pinguicolla, with the last confident sighting in 1969, raising the possibility of the first extinction of a reptile on mainland Australia. However, our results are equivocal as to whether T. pinguicolla is extant or extinct, emphasizing the immediate imperative for continued surveys to locate any remaining populations of T. pinguicolla. We also highlight the need for a full revision of conservation management plans for all the grassland earless dragons.

Bacterioplankton Community Composition Along Environmental Gradients in Lakes From Byers Peninsula (Maritime Antarctica) as Determined by Next-Generation Sequencing.

This study comprises the first attempt to describe the planktonic bacterial communities of lakes from Byers Peninsula, one of the most significant limnological districts in the Maritime Antarctica, leveraging next-generation sequencing (NGS) technologies. For the survey, we selected 7 lakes covering the environmental gradient from inland to coastal lakes, some of them sampled both in surface and deep waters. Analysis provided just over 85,000 high quality sequences that were clustered into 864 unique Zero-radius Operational Taxonomic Units (ZOTUs) (i.e., 100% sequence similarity). Yet, several taxonomic uncertainties remained in the analysis likely suggesting the occurrence of local bacterial adaptations. The survey showed the dominance of the phyla Proteobacteria and Bacteroidetes. Among the former, the Gammaproteobacteria class, more specifically the order Betaproteobacteriales, was the dominant group, which seems to be a common trend in nutrient-limited Antarctic lakes. Most of the families and genera ubiquitously detected belonging to this class are indeed typical from ultra-oligotrophic environments, and commonly described as diazotrophs. On the other hand, among the members of the phylum Bacteroidetes, genera such as Flavobacterium were abundant in some of the shallowest lakes, thus demonstrating that also benthic and sediment-associated bacteria contributed to water bacterial assemblages. Ordination analyses sorted bacterial assemblages mainly based on the environmental gradients of nutrient availability and conductivity i.e., salinity. However, transient bacterial associations, that included the groups Clostridiaceae and Chloroflexi, also occurred as being forced by other drivers such as the influence of the nearby fauna and by the airborne microorganisms. As we intended, our NGS-based approach has provided a much greater resolution compared to the previous studies conducted in the area and confirmed to a large extent the previously obtained patterns, thus reinforcing the view of Byers as a hotspot of microbial biodiversity within Antarctica. This high microbial diversity allows the use of these aquatic ecosystems and their bacterial assemblages as sentinels for the monitoring of adaptive responses to climate change in this rapidly warming area.

Ending a 175-year taxonomic uncertainty: Description of Staurosirella neopinnata sp. nov. (Bacillariophyta) to accommodate Fragilaria pinnata, a highly misconstrued taxon with a purported worldwide distribution

Fragilaria pinnata Ehrenberg is actually a member of the genus Denticula Kützing. However, due to a drift of its taxonomic concept, there is now a “floating” idea of F. pinnata as an araphid diatom associated to Staurosirella D.M.Williams &amp; Round (as S. pinnata (Ehrenberg) D.M.Williams &amp; Round). Upon investigation of the nomenclatural history of F. pinnata and examination of type material of Staurosirella mutabilis (W.Smith) E.Morales &amp; Van de Vijver (= Odontidium mutabile (W.Smith) Kützing), a commonly reported synonym for S. pinnata, it became evident that the material studied in depth by Haworth (1974, 1975, 1976) is the most suitable to give a formal taxonomic concept to that floating idea. For this purpose, we describe a new species, Staurosirella neopinnata, from the mentioned material. This diatom is distinguished by the raised axial area and virgae, and the solid, apically flattened spines, originating from two or three points on the virgae. The largest population found in the analyzed material corresponds to a depth of 208 cm in a sediment core (early Flandrian, ca. 10226 +/- 190 YBP) from Loch Borralan, Scotland, a shallow lake exposed to wind disturbance and containing, at that depth, a diatom assemblage characterized by a high density of S. neopinnata and benthic forms that are alkaliphilous, halobion and current indifferent, non-aerophilic and non-cryophilic. Through a review of electron microscopy images in the literature, we preliminarily establish that the new taxon has a Holarctic distribution and that the great majority of F. pinnata reports from other biogeographic realms correspond to different, as yet formally undescribed species.

The extinction risk of New Zealand chondrichthyans

Abstract The national extinction risk of 103 New Zealand chondrichthyans (sharks, rays, and chimaeras), ~10% of the global chondrichthyan fauna, was evaluated for the first time using the International Union for Conservation of Nature Red List of Threatened Species Categories and Criteria. Across 32 families, 103 species were assessed. New Zealand holds a high degree of species endemism (20%) with deepwater species dominating the fauna (77%). Sharks were the most speciose group with 68 species (66%), followed by 24 rays (23%), and 11 chimaeras (10%). Most species were assessed as Least Concern (60%, 62 species) or Data Deficient (32%, 33 species), with four (3.8%) species listed as Near Threatened and four (3.8%) in a threatened category (Vulnerable, Endangered, Critically Endangered). Threatened species are all oceanic pelagic, of which two are only visitors to New Zealand waters, and their status the result of broader regional declines. These results are in stark contrast to other recent regional assessments in Europe and the Arabian Sea and adjacent areas, where up to half of species were listed in a threatened category. However, given New Zealand's extensive deepwater fishing effort and rapid collapses of deepwater chondrichthyan fisheries elsewhere, it is possible that New Zealand populations of many deepwater species are the remnants of previously reduced populations that are now at a low, yet stable level. Ongoing species‐level catch monitoring will be required to ensure these species do not become threatened. Recommendations for future research and conservation efforts include resolving taxonomic uncertainties, understanding habitat use, and increasing regional collaborations to better understand the effects of fishing on wider‐ranging species.