Putative Species Research Articles

Molecular phylogenetics and diversity of the Himalayan shrew ( Soriculus nigrescens Gray, 1842) (Eulipotyphla, Soricidae) in Southwest China

The Himalayan shrew, Soriculus nigrescens Gray, 1842, belongs to the monotypic genus Soriculus, which is distributed mainly in the Himalayan region. Previous authors have studied its classification based on morphological and molecular data. However, no comprehensive study of the diversity and phylogeny of this species has been performed. In this study, we investigated the molecularphylogeny, genetic diversity, and species divergence of S. nigrescens based on one mitochondrial gene and three nuclear genes. A total of 124 samples from 27 sites in Southwest China were analyzed. Our molecular phylogenetic analyses and species divergence reveal non-monophyly of Soriculus, potentially representing two genera and three clades. Populations from Yunnan (Clade YN) represent the subspecies S. n. minors and should recover the full species status. Populations from Himalayas (Clade A) represent the species S. nigrescens, while populations from southeastern Nyenchen Tanglha Mountains and southern Himalayas (Clade B) represent a new cryptic and unnamed species. Species delimitation analyses and deep genetic distance analysis clearly support the species status of these three evolving clades. The putative new genus and cryptic species should be studied and identified in the future using a more extensive sampling combined with a comprehensive morphological and phylogenetic analysis.

Dianthus × belkinii (Caryophyllaceae), a new hybrid taxon from Altai

Dianthus × belkinii is an intersectional hybrid newly described from the Republic of Altai (Talduair massif). This taxon was also noted in Mongolia (Bayan-Ulegei aimag). The article describes the morphological features of the new taxon and discusses its relationship with parental species. The described hybrid has intermediate morphological features between the parental species, most notable are the fringed corollas. The stems are sparsely branched, relatively tall and similar to those of D. superbus. The calyx lobes and bracts are transitional between D. superbus and D. versicolor. The limb of the corolla is cut for ⅓–¼ of its length into a few lobes. Cytometry data showed an identical ploidy level of the new taxon and its putative parent species. The average value of the relative DNA content is almost intermediate, however, somewhat closer to D. versicolor. The ITS sequences of D. × belkinii show characteristic double peaks, which may point to a hybridogeneous origin of the plants. Identical chloroplast DNA sequences with D. versicolor but differences to D. superbus suggests that D. versicolor may be the maternal parent of this hybrid. Based on these polymorphisms, it is possible to state that the ITS sequence and D. versicolor × superbus itself are of a hybrid nature, where D. versicolor and D. superbus are the parent forms.

Effects of Microbial Communities on Elevational Gradient Adaptation Strategies of Pinus yunnanensis Franch. and Pinus densata Mast. in a Mixed Zone

Pinus densata Mast. is considered a homoploid hybrid species that originated from the putative parent species Pinus tabuliformis Carr. and Pinus yunnanensis Franch., but the mechanism of the adaptive differentiation of P. densata and its parents in native habitats has not been reported. Therefore, the overlapping distribution areas between P. densata and P. yunnanensis in the heart of the Hengduan Mountains were chosen. The adaptive differentiation mechanism of the homoploid hybrids and their parents with respect to the elevational gradient was studied based on the morphological features and the different strategies of recruiting endophytic microbial communities from the rhizosphere soil. The results showed that (1) the height and diameter at breast height were the greatest at 2600 m and 2900 m, and from 2700 m to 2900 m, three-needle pines (P. yunnanensis-like type) transitioned into two-needle pines (P. densata-like type). (2) The recruitment of rhizosphere microbial communities was driven by the C, N, P and pH values which showed significant elevation features. (3) There was a significant difference in the recruitment strategies of endophytes between the P. yunnanensis-like type and P. densata-like type. Pinus densata mainly reduced the recruitment of Mucoromycota (fungi) and increased the recruitment of Proteobacteria (bacteria), which may be related to environmental adaptability, quorum sensing and the metabolism of auxiliary factors and vitamins at high elevations. (4) The root endophytic microbiome was enriched in the rare groups from the rhizosphere soil microbial pool. The results of this study provide new insights and new ideas for environmental adaptability and differentiation in homoploid hybrid speciation.

Genomes of four Streptomyces strains reveal insights into putative new species and pathogenicity of scab-causing organisms

Genomes of four Streptomyces isolates, two putative new species (Streptomyces sp. JH14 and Streptomyces sp. JH34) and two non thaxtomin-producing pathogens (Streptomyces sp. JH002 and Streptomyces sp. JH010) isolated from potato fields in Colombia were selected to investigate their taxonomic classification, their pathogenicity, and the production of unique secondary metabolites of Streptomycetes inhabiting potato crops in this region. The average nucleotide identity (ANI) value calculated between Streptomyces sp. JH34 and its closest relatives (92.23%) classified this isolate as a new species. However, Streptomyces sp. JH14 could not be classified as a new species due to the lack of genomic data of closely related strains. Phylogenetic analysis based on 231 single-copy core genes, confirmed that the two pathogenic isolates (Streptomyces sp. JH010 and JH002) belong to Streptomyces pratensis and Streptomyces xiamenensis, respectively, are distant from the most well-known pathogenic species, and belong to two different lineages. We did not find orthogroups of protein-coding genes characteristic of scab-causing Streptomycetes shared by all known pathogenic species. Most genes involved in biosynthesis of known virulence factors are not present in the scab-causing isolates (Streptomyces sp. JH002 and Streptomyces sp. JH010). However, Tat-system substrates likely involved in pathogenicity in Streptomyces sp. JH002 and Streptomyces sp. JH010 were identified. Lastly, the presence of a putative mono-ADP-ribosyl transferase, homologous to the virulence factor scabin, was confirmed in Streptomyces sp. JH002. The described pathogenic isolates likely produce virulence factors uncommon in Streptomyces species, including a histidine phosphatase and a metalloprotease potentially produced by Streptomyces sp. JH002, and a pectinesterase, potentially produced by Streptomyces sp. JH010. Biosynthetic gene clusters (BGCs) showed the presence of clusters associated with the synthesis of medicinal compounds and BGCs potentially linked to pathogenicity in Streptomyces sp. JH010 and JH002. Interestingly, BGCs that have not been previously reported were also found. Our findings suggest that the four isolates produce novel secondary metabolites and metabolites with medicinal properties.

High Andean Steppes of Southern Chile Contain Little-Explored Peltigera Lichen Symbionts

Peltigera lichens can colonize extreme habitats, such as high-elevation ecosystems, but their biodiversity is still largely unknown in these environments, especially in the southern hemi- sphere. We assessed the genetic diversity of mycobionts and cyanobionts of 60 Peltigera lichens collected in three high Andean steppes of southern Chile using LSU, β-tubulin, COR3 and ITS loci for mycobionts, and SSU and rbcLX loci for cyanobionts. We obtained 240 sequences for the different mycobiont markers and 118 for the cyanobiont markers, including the first report of β-tubulin sequences of P. patagonica through modifying a previously designed primer. Phylogenetic analyses, ITS scrutiny and variability of haplotypes were used to compare the sequences with those previously reported. We found seven mycobiont species and eleven cyanobiont haplotypes, including considerable novel symbionts. This was reflected by ~30% of mycobionts and ~20% of cyanobionts haplotypes that yielded less than 99% BLASTn sequence identity, 15 new sequences of the ITS1-HR, and a putative new Peltigera species associated with 3 Nostoc haplotypes not previously reported. Our results suggest that high Andean steppe ecosystems are habitats of unknown or little-explored lichen species and thus valuable environments to enhance our understanding of global Peltigera biodiversity.

Spiranthes hachijoensis (Orchidaceae), a new species within the S. sinensis species complex in Japan, based on morphological, phylogenetic, and ecological evidence

The systematics of the Old World Spiranthes sinensis (Pers.) Ames species complex (Orchidaceae) has been complicated by its wide distribution and morphological variations. Within the species complex, S. australis Lindl. has been generally accepted as the only Spiranthes Rich. species distributed on the Japanese mainland. The present study provides morphological, phylogenetic, and ecological evidence for the recognition of S. hachijoensis Suetsugu as a new species of the S. sinensis species complex on the Japanese mainland. Spiranthes hachijoensis is morphologically similar to S. hongkongensis S.Y. Hu & Barretto and S. nivea T.P. Lin & W.M. Lin, sharing a degenerated rostellum, pollinia without a viscidium, and distinctly trilobed stigma. However, the taxon can be morphologically distinguished from S. hongkongensis by its glabrous rachis, ovaries, and sepals, and from S. nivea by its papillate labellum disc, larger papillate basal labellum callosities, and glabrous rachis, ovaries, and sepals. The autogamy and flowering phenology (i.e., earlier flowering) of S. hachijoensis are most likely responsible for premating isolation from the sympatric S. australis. A MIG-seq-based high-throughput molecular analysis indicated that the genetic difference between S. hachijoensis and its putative sister species S. sinensis is comparable to, or even greater than, the genetic difference between pairs of other species within the S. sinensis species complex. Our multifaceted approach strongly supports the recognition of S. hachijoensis as a morphologically, phenologically, phylogenetically, and ecologically distinct species.

Exceptional levels of species discovery ameliorate inferences of the biogeography and diversification of an Afrotropical catfish family

Endeavours in species discovery, particularly the characterisation of cryptic species, have been greatly aided by the application of DNA molecular sequence data to phylogenetic reconstruction and inference of evolutionary and biogeographic processes. However, the extent of cryptic and undescribed diversity remains unclear in tropical freshwaters, where biodiversity is declining at alarming rates. To investigate how data on previously undiscovered biodiversity impacts inferences of biogeography and diversification dynamics, we generated a densely sampled species-level family tree of Afrotropical Mochokidae catfishes (220 valid species) that was ca. 70 % complete. This was achieved through extensive continental sampling specifically targeting the genus Chiloglanis a specialist of the relatively unexplored fast-flowing lotic habitat. Applying multiple species-delimitation methods, we report exceptional levels of species discovery for a vertebrate genus, conservatively delimiting a staggering ca. 50 putative new Chiloglanis species, resulting in a near 80 % increase in species richness for the genus. Biogeographic reconstructions of the family identified the Congo Basin as a critical region in the generation of mochokid diversity, and further revealed complex scenarios for the build-up of continental assemblages of the two most species rich mochokid genera, Synodontis and Chiloglanis. While Syndontis showed most divergence events within freshwater ecoregions consistent with largely in situ diversification, Chiloglanis showed much less aggregation of freshwater ecoregions, suggesting dispersal as a key diversification process in this older group. Despite the significant increase in mochokid diversity identified here, diversification rates were best supported by a constant rate model consistent with patterns in many other tropical continental radiations. While our findings highlight fast-flowing lotic freshwaters as potential hotspots for undescribed and cryptic species diversity, a third of all freshwater fishes are currently threatened with extinction, signifying an urgent need to increase exploration of tropical freshwaters to better characterise and conserve its biodiversity.

Abstract 22: The Effects of Randomized Cocoa Extract and Multivitamins on the Gut Microbiome: A Pilot Study in COSMOS

Background: The COcoa Supplement and Multivitamin Outcomes Study (COSMOS) is a recently completed randomized, double-blind, placebo-controlled, 2x2 factorial trial of a multivitamin and cocoa extract supplement (containing 500 mg/d flavanols) in 21,442 older adults. In view of favorable effects of multivitamins on cognition and promising signals for cardiovascular risk reduction with cocoa extract, we conducted a pilot study to explore whether these interventions affected gut microbial composition and function. Methods: We conducted deep shotgun metagenomic sequencing in 30 COSMOS participants using fecal samples collected at baseline and year 2. We performed taxonomic profiling using MetaPhlAn2 and functional profiling using HUMAnN2. After proper quality filtering, we analyzed effects of both interventions on 2-year changes in microbial features, adjusting for age, sex, and body mass index. Results: Cocoa extract supplementation significantly altered the overall gut microbial taxonomic compositions from baseline to year 2, and explained 5.5% of the variance in the 2-year changes in relative abundance of all microbial species ( P =0.008). We further found that randomized cocoa extract supplementation altered the relative abundance of a few microbial species, including those previously linked to anti-inflammatory and cardiometabolic benefits (e.g., Akkermansia muciniphila , nominal P <0.05), and several microbial super pathways (including pyrimidine ribonucleotides de novo biosynthesis, FDR=0.03, and 28 other pathways with nominal P <0.05). Randomized multivitamin use did not significantly affect 2-year changes in alpha or beta diversity, but altered the abundance a few putative bacterial species and functional pathways (nominal P <0.05). Summary: Our pilot study suggests that cocoa extract and multivitamin supplementation in COSMOS may alter the gut microbiome and influence pathways relevant to health, emphasizing the need for larger studies that allow for more detailed investigations.

Biogeography and Genetic Diversity of Terrestrial Mites in the Ross Sea Region, Antarctica.

Free-living terrestrial mites (Acari) have persisted through numerous glacial cycles in Antarctica. Very little is known, however, of their genetic diversity and distribution, particularly within the Ross Sea region. To redress this gap, we sampled mites throughout the Ross Sea region, East Antarctica, including Victoria Land and the Queen Maud Mountains (QMM), covering a latitudinal range of 72-85 °S, as well as Lauft Island near Mt. Siple (73 °S) in West Antarctica and Macquarie Island (54oS) in the sub-Antarctic. We assessed genetic diversity using mitochondrial cytochrome c oxidase subunit I gene sequences (COI-5P DNA barcode region), and also morphologically identified voucher specimens. We obtained 130 sequences representing four genera: Nanorchestes (n = 30 sequences), Stereotydeus (n = 46), Coccorhagidia (n = 18) and Eupodes (n = 36). Tree-based analyses (maximum likelihood) revealed 13 genetic clusters, representing as many as 23 putative species indicated by barcode index numbers (BINs) from the Barcode of Life Datasystems (BOLD) database. We found evidence for geographically-isolated cryptic species, e.g., within Stereotydeus belli and S. punctatus, as well as unique genetic groups occurring in sympatry (e.g., Nanorchestes spp. in QMM). Collectively, these data confirm high genetic divergence as a consequence of geographic isolation over evolutionary timescales. From a conservation perspective, additional targeted sampling of understudied areas in the Ross Sea region should be prioritised, as further diversity is likely to be found in these short-range endemic mites.

Deep mtDNA Sequence Divergences and Possible Species Radiation of Whip Spiders (Arachnida, Amblypygi, Phrynidae, Phrynus/Paraphrynus) among Caribbean Oceanic and Cave Islands

Islands—whether classic oceanic islands or habitat islands such as isolated thermal vents, mountain tops, or caves—often promote the diversification of lineages that colonize them. We examined CO1 mtDNA sequence divergences within the tailless whip spider genus Phrynus Lamarck, 1809 (Amblypygi: Phrynidae) among oceanic islands and among cave ’islands´ distributed across the Caribbean archipelago and on the continental mainland. The significance of this study lies in the extensive taxon sampling of a supposedly depauperate lineage (considering its age), over a large proportion of its geographical range, and the discovery of deep mtDNA sequence divergences. We sampled thousands of specimens—and sequenced 544, including six outgroup species—across 173 localities on 17 islands (135 localities) and five countries on the North to South American mainland (38 localities), including a total of 63 caves. Classical taxonomy identified ten named Phrynus and two Paraphrynus Moreno, 1940 species. Paraphrynus seems to be paraphyletic and nested in Phrynus. Uncorrected genetic distances within named species and among morphological species ranged up to 15% and 19%, respectively. Geographic distances explained a significant portion of genetic distances on islands (19%, among both subterranean and epigean specimens), and for epigean specimens on the mainland (27%). Species delimitation analyses indicated that the 12 named species harbored from 66 to well over 100 putative species. The highest number of species was indicated by the GMYC method (114 species) while the Bayesian Poisson tree processes (bPTP) and the BP&P relying on the Markov chain Monte Carlo Bayesian Phylogenetic model estimated an upper level of 110 species. On the other hand, the recently recommended and relatively conservative distance-based (phylogeny free) ASAP model has the greatest support for 73 species. In either case, nearly all putative species are tightly limited to a single locality, often a small cave system, and sometimes to the surrounding epigean area. Caribbean Phrynus diversity has likely been vastly underestimated, likely due to both morphological crypsis and the ignorance of Caribbean cave fauna. Although mtDNA sequences can suggest species limits, nuclear DNA sequencing and detailed morphological research are necessary to corroborate them and explore whether this phenomenon constitutes species radiation or perhaps just mtDNA divergences as a consequence of, for example, stationary females and actively dispersing males.

Vector communities under global change may exacerbate and redistribute infectious disease risk.

Vector-borne parasites may be transmitted by multiple vector species, resulting in an increased risk of transmission, potentially at larger spatial scales compared to any single vector species. Additionally, the different abilities of patchily distributed vector species to acquire and transmit parasites will lead to varying degrees of transmission risk. Investigation of how vector community composition and parasite transmission change over space due to variation in environmental conditions may help to explain current patterns in diseases but also informs our understanding of how patterns will change under climate and land-use change. We developed a novel statistical approach using a multi-year, spatially extensive case study involving a vector-borne virus affecting white-tailed deer transmitted by Culicoides midges. We characterized the structure of vector communities, established the ecological gradient controlling change in structure, and related the ecology and structure to the amount of disease reporting observed in host populations. We found that vector species largely occur and replace each other as groups, rather than individual species. Moreover, community structure is primarily controlled by temperature ranges, with certain communities being consistently associated with high levels of disease reporting. These communities are essentially composed of species previously undocumented as potential vectors, whereas communities containing putative vector species were largely associated with low levels, or even absence, of disease reporting. We contend that the application of metacommunity ecology to vector-borne infectious disease ecology can greatly aid the identification of transmission hotspots and an understanding of the ecological drivers of parasite transmission risk both now and in the future.

The anthropogenic threat for insular microcrustacean fauna (Copepoda and Cladocera) – the case of Madeira Island

Substantial loss of biodiversity and the proliferation of invasive alien species can occur due to land cover anthropogenic transformations on islands. However, the effect of anthropogenic habitat modifications on the distribution of insular freshwater microcrustaceans is unknown. In the present paper, we examine the consequences of human activity on the insular diversity of microcrustaceans in the context of the theories of island biogeography and intermediate disturbances. The samples were collected in Madeira Island at 38 freshwater sampling sites with different anthropopressure. Morphology-based species identification of the copepods and cladocerans was supplemented with genetic analysis (COI) in some species. To estimate the species richness of the island, rarefaction, and extrapolation methods were used. Canonical Correspondence Analysis (CCA) was applied to assess the influence of geospatial and environmental variables on the species distribution. A total of 20 species belonging to six families were identified, of which 16 species are new to Madeira. There was low similarity between the fauna recorded and known previously on the island. The observed species richness was higher than the predictions by the island biogeography models for Madeira. CCA revealed a strong influence of anthropogenic land use on crustaceans. Anthropogenic transformations locally led to the depletion of fauna, but on the island scale they contributed to the increase of species richness including seven putative alien species. An increase in the artificial land cover and a decrease in the forest areas could lead to a further shift in the domination of non-indigenous microcrustaceans.

First insights into the gut microbiome of Diatraea saccharalis: From a sugarcane pest to a reservoir of new bacteria with biotechnological potential

A country’s biodiversity is a key resource for the development of a sustainable bioeconomy. However, often the most biodiverse countries on the planet hardly profit from their biological diversity. On the contrary, occasionally components of that biodiversity become a threat to society and its food sustainability. That is the case of the sugarcane borer Diatraea saccharalis. Here, the analysis of the bacteria associated with the digestive tract of D. saccharalis reveals a rich and diverse microbiota. Two types of diets were analyzed under laboratory conditions. The metataxonomic analysis revealed a number of taxa common to most of the larval pools analyzed with relative abundances exceeding 5%, and five families of bacteria which have also been reported in the gut of another Lepidoptera. A large fraction of microorganisms detected by amplicon sequencing were considered to be rare and difficult to cultivate. However, among the cultivable microorganisms, 12 strains with relevant biotechnological features were identified. The strain that showed the highest cellulolytic activity (GCEP-101) was genome sequenced. The analysis of the GCEP-101 complete genome revealed that the values of 16S rRNA identity, the Average Nucleotide Identity, and the digital DNA–DNA hybridization place the strain as a candidate for a new species within the genus Pseudomonas. Moreover, the genome annotation of the putative new species evidenced the presence of genes associated with cellulose degradation, revealing the hidden potential of the pest as a reservoir of biotechnologically relevant microorganisms.

Taxonomic insights and evolutionary history in East Asian terrestrial slugs of the genus Meghimatium

East Asia, specifically the Japanese Archipelago, is a biodiversity hotspot of both vertebrates and invertebrates. Mollusks represent a burst of species diversity in this region due to the effects of biotic and abiotic factors on their morphological traits, such as shell shape and size. However, the evolutionary history of terrestrial slugs in East Asia remains unknown. In the present study, we investigated the molecular phylogeny of terrestrial slugs of the genus Meghimatium. This genus includes three described and eight undescribed species, and our study used all except for two. Based on phylogeny and the species delimitation tests, the genus Meghimatium was split into many putative species, suggesting higher species diversity than previously thought based on morphological and anatomical studies and that almost undescribed species may be inappropriate. Therefore, morphological traits, such as body size and colour, conventionally considered for classification may easily vary or be similar across geographic region. Moreover, the divergence time of this genus is almost concordant with the geographical time scale of the formation of the Japanese mainland. Our findings suggest that molecular phylogenetics helps classify Japanese Meghimatium slugs, but comprehensive taxonomic revisions using multi-locus analyses are needed.

Temporal Dynamics and Performance Association of the Tetrasphaera-Enriched Microbiome for Enhanced Biological Phosphorus Removal

Tetrasphaera have been recently identified based on the 16S ribosomal RNA (rRNA) gene as among the most abundant polyphosphate-accumulating organisms (PAOs) in global full-scale wastewater treatment plants (WWTPs) with enhanced biological phosphorus removal (EBPR). However, it is unclear how Tetrasphaera PAOs are selectively enriched in the context of the EBPR microbiome. In this study, an EBPR microbiome enriched with Tetrasphaera (accounting for 40% of 16S sequences on day 113) was built using a top-down design approach featuring multicarbon sources and a low dosage of allylthiourea. The microbiome showed enhanced nutrient removal (phosphorus removal ∼85% and nitrogen removal ∼80%) and increased phosphorus recovery (up to 23.2 times) compared with the seeding activated sludge from a local full-scale WWTP. The supply of 1 mg·L−1 allylthiourea promoted the coselection of Tetrasphaera PAOs and Microlunatus PAOs and sharply reduced the relative abundance of both ammonia oxidizer Nitrosomonas and putative competitors Brevundimonas and Paracoccus, facilitating the establishment of the EBPR microbiome. Based on 16S rRNA gene analysis, a putative novel PAO species, EBPR-ASV0001, was identified with Tetrasphaera japonica as its closest relative. This study provides new knowledge on the establishment of a Tetrasphaera-enriched microbiome facilitated by allylthiourea, which can be further exploited to guide future process upgrading and optimization to achieve and/or enhance simultaneous biological phosphorus and nitrogen removal from high-strength wastewater.

Monostephanostomum mesospinosum (Digenea: Acanthocolpidae) Infecting the Coastal Trevally Carangoides caeruleopinnatus (Carangiformes: Carangidae) from the Marine Water off Saudi Arabia

Background: Carangids, like any other fish, can become infected with a variety of external and internal parasites. Little information on parasite infestations in these fish species is known. This study aimed to provide light on parasites that infect caragnids in Saudi Arabia. Methods: A total of 20 Carangoides caeruleopinnatus specimens were collected from the Red Sea (Saudi Arabia) and then examined for the presence of digenetic trematodes. Parasitic species were isolated and studied morphologically by using light microscopic examination and molecularly via the partial sequencing of 18S rRNA and 28S rRNA genes. Result: Only one parasitic species has been identified. This parasite is morphologically and morphometric compatible with previously Monostephanostomum mesospinosum, identified from Carangoides malabaricus in VSK, BOB. Phylogeny revealed that these putative acanthocolpid species nested well within a clade clustering Monostephanostomum species, which along with morphological data, suggests it is a member of the genus Monostephanostomum. Query sequences showed identities of 97.99% and 97.98% for 18S (EF506762.1.1) and 28S rRNA (EF506763.1) of Monostephanostomum nolani, respectively. This study reflects the third account of this genus as endoparasitic taxa of various carangid fish, as well as providing novel DNA data for this species.

Genetic population structures of common scavenging species near hydrothermal vents in the Okinawa Trough

Deep-sea mining of hydrothermal deposits off the coast of Japan is currently under consideration, and environmental baseline studies of the area are required to understand possible impacts. The aim of this study is to clarify population structures of dominant benthic megafaunal species near hydrothermal vent fields in the Okinawa Trough, using a population genetics approach. We examined dominant deep-sea scavenging species including eels, several amphipods, and a decapod and performed population genetic analyses based on the mitochondrial cytochrome c oxidase subunit I region. Several sites were sampled within Okinawa Trough to examine intra-population diversity while two other locations 1400–2400 km away were chosen for inter-population comparisons. For synaphobranchid eels Simenchelys parasitica and Synaphobranchus kaupii, our results showed significant intra-population diversity but no inter-population genetic differentiation, suggesting strong genetic connectivity and/or large population sizes. In addition, single nucleotide polymorphism analysis also confirmed strong genetic connectivity for Simenchelys parasitica. Among scavenging amphipods, we detected seven putative species using molecular phylogenetic analysis. We evaluated population structures of the most abundant species of amphipods and a decapod species (Nematocarcinus lanceopes). Our results provide basic information on the genetic population structures of benthic megafaunal species near hydrothermal vent fields, which can be used to select candidate species for future connectivity analysis with high-resolution genetic markers and aid understanding of the potential population impacts of environmental disturbances.

A Study in Scarlet: Integrative Taxonomy of the Spider Genus Loureedia (Araneae: Eresidae)

The eresid spider genus Loureedia (Miller et al., 2012) was described a decade ago, despite its type species being described in the mid-19th century, which illuminates the difficulties in obtaining specimens. The genus was initially described as monotypic. Ever since, four other species have been assigned to Loureedia, including three newly discovered ones. Primarily due to the extravagant appearance of the males, stories about the discovery of species of Loureedia have been the subject of relatively wide media coverage over the years, leading to numerous new populations and putative undescribed species being documented by naturalists and citizen scientists. These species, although bearing distinct differences in their coloration patterns, typically vary only slightly in the structure of their copulatory organs, the primary traits used in spider systematics. This highlights an important taxonomic problem: while it is easy to diagnose the genus or recognize the species that belong to it, it is challenging to differentiate the species from one another, particularly when using only a single line of evidence. In this paper, we have tackled this issue using an integrative approach, i.e., a combination of molecular markers (the mitochondrial COI) and traditional morphological characters. The effects of different observational angles on the perceived shape of the conductor are discussed. Except for one species, we obtained DNA data of all members of the genus. Based on these data, the first phylogeny for Loureedia is presented, and two North African species, Loureedia maroccana (Gál et al., 2017) and Loureedia jerbae (El-Hennawy, 2005), are revalidated from synonymy. The distribution records of all described species are mapped.

A note on cetaceans off Kiribati and Tuvalu from a research cruise in October 2010

This paper summarises the results of a sighting survey conducted around the Gilbert Islands (Kiribati) and Tuvalu Islands (Tuvalu) in the central Pacific Ocean between 3 and 17 October 2010. This was the first systematic collection of cetacean sighting data in this region. The main objective of the survey was to investigate the occurrence and distribution of cetaceans around Kiribati and Tuvalu. In addition biopsy samples were obtained to investigate the species identity of Bryde’s-whale-like baleen whales through genetic analyses and to assess feeding ecology of cetaceans in the survey area through the examination of fatty acids. The survey was carried out using a sighting survey vessel, which covered a total of 1,012 n.miles (≈1,875km). A total of 24 schools (640 individuals) of cetaceans was sighted: three schools (five individuals) of Bryde’s-whale-like baleen whales, one school (nine individuals) of sperm whales (Physeter macrocephalus), one school (six individuals) of killer whales (Orcinus orca), one school (14 individuals) of short finned pilot whales (Globicephala macrorhynchus), one school (two individuals) of false killer whales (Pseudorca crassidens), eight schools (483 individuals) of spinner dolphins (Stenella longirostris), and one school (70 individuals) of striped dolphins (Stenella coeruleoalba). Mitochondrial DNA (mtDNA) analyses based on the biopsy samples identified two of the Bryde’s-whale-like whales sighted, as of the putative species Balaenoptera brydei. Compositions of fatty acids of Bryde’s and killer whales are presented. The survey provided new information on the distribution and fatty-acid composition of cetaceans around Kiribati and Tuvalu.

Diversity of viroids infecting grapevines in the South African Vitis germplasm collection.

Seven viroid species and one putative viroid species have been reported to infect grapevine namely, hop stunt viroid (HSVd), grapevine yellow speckle viroid 1 (GYSVd-1), grapevine yellow speckle viroid 2 (GYSVd-2), Australian grapevine viroid (AGVd), Japanese grapevine viroid (JGVd), grapevine latent viroid (GLVd), and citrus exocortis viroid (CEVd), as well as a grapevine hammerhead viroid-like RNA (GHVd), so far. In this study, RNA sequence (RNA-Seq) data, from 229 Vitis accessions from the field-maintained vineyard of the South African Vitis germplasm collection, were analysed to determine the diversity of the viroids present. Five of the seven known grapevine-infecting viroids and one putative grapevine-infecting viroid species were very commonly found, with 214 of the 229 samples containing at least one viroid species. HSVd, GYSVd-1, GYSVd-2, AGVd, and JGVd, as well as GHVd, were identified in the RNA-Seq data of the samples and confirmed using RT-PCR and Sanger sequencing. The HSVd sequences indicated the presence of two variants, with one showing multiple nucleotide insertions. AGVd and GYSVd-2 did not display significant sequence diversity, confirming past international studies. GYSVd-1 occurs as four major variants worldwide and representatives of all four variants were identified in this vineyard. This is the first report on the diversity of viroids infecting grapevine in South Africa and the first report of JGVd outside of Japan and GHVd in South Africa. Further studies are needed to fully assess the population and to identify potentially new viroid species.