DNA sequence-based identification of Fusarium: A work in progress

Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent’s identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise over 400 phylogenetically distinct species (i.e., phylospecies), with over 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the non-redundant NCBI nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1 and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue (Torres-Cruz et al. 2022), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.

Nanopore adaptive sampling for mitogenome sequencing and bloodmeal identification in hematophagous insects

Blood-feeding insects are important vectors for an array of zoonotic pathogens. Despite significant research focused on well-documented insect vectors of One Health importance, resources for molecular species identification of a large number of hematophagous arthropods are limited. Advancements in next-generation sequencing technologies provide opportunities for targeting mitochondrial genomes of blood-feeding insects, as well as their bloodmeal hosts. This dual approach holds great promise for elucidating complex disease transmission pathways and enhancing the molecular resources for the identification of cryptic insect species. To this end, we leveraged the newly developed Oxford Nanopore Adaptive Sampling (NAS) pipeline to dually sequence the mitogenomes of hematophagous insects and their bloodmeals. Using NAS, we sequenced the entire mitogenomes of Aedes vexans, Culex restuans, Culex territans, and Chrysops niger and successfully identified bloodmeal hosts of Chrysops niger, Culex restuans, and Aedes trivittatus. We show that NAS has the utility to simultaneously molecularly identify blood-feeding insects and characterize disease transmission pathways through bloodmeal host identification. Moreover, our data indicate NAS can facilitate a wide array of molecular systematic studies through novel 'phylogenetic capture' methods. We conclude the NAS approach has great potential for informing global One Health initiatives centered on the mitigation of vector-borne disease through dual vector and bloodmeal identification.

Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean

Eurythenes S.I. Smith in Scudder, 1882 (Crustacea: Amphipoda) are prevalent scavengers of the benthopelagic community from bathyal to hadal depths. While a well-studied genus, molecular systematic studies have uncovered cryptic speciation and multiple undescribed lineages. Here, we apply an integrative taxonomic approach and describe the tenth species, Eurythenes atacamensis sp. nov., based on specimens from the 2018 Atacamex and RV Sonne SO261 Expeditions to the southern sector of the Peru-Chile Trench, the Atacama Trench (24–⁠21°S). Eurythenes atacamensis sp. nov. is a large species, max. observed length 83.2 mm, possesses diagnostic features, including a short gnathopod 1 palm and a chelate gnathopod 2 palm, and a distinct genetic lineage based on a 16S rRNA and COI phylogeny. This species is a dominant bait-attending fauna with an extensive bathymetric range, spanning from 4974 to 8081 m. The RV Sonne SO261 specimens were recovered along a 10-station transect from abyssal to hadal depths and further examined for demographic and bathymetric-related patterns. Ontogenetic vertical stratification was evident across the trench axis, with only juveniles present at abyssal depths (4974–6025 m). Total length-depth analysis revealed that the size of females was unrelated to depth, whereas juveniles followed a sigmoidal relationship with a step-up in size at depths >7200 m. Thus, these bathymetric trends suggest that juveniles and females employ differing ecological strategies in subduction trench environments. This study highlights that even dominant and ecologically important species are still being discovered within the abyssal and hadal environments. Continued systematic expeditions will lead to an improved understanding of the eco-evolutionary drivers of speciation in the world’s largest ecosystem.

Molecular Systematic Investigations of Three Fin Fish Cichlid Species of Oreochromis niloticus (Nile Tilapia), Genetically Improved Farmed Tilapia (GIFT) and Astronotus ocellatus (Oscar Cichlid)

Fisheries in India contribute significantly to the total GDP of agriculture and earn significant foreign exchange. Aquaculture is playing an important role in India and is bestowed with a huge biodiversity of aquatic organisms. India ranks second in total fish production in the world. Nile tilapia has become the world’s second most popular farmed fish, after carps. Oscars is a popular aquarium fish around the world. In the present study, efforts were made to analyze the extent of divergence or similarity among three cichlid finfishes (Nile Tilapia, GIFT Tilapia, and Oscar Cichlid) using molecular biology techniques such as Random Amplification of Polymorphic DNA (RAPD) and Restriction Fragment Length Polymorphism (RFLP). The Phylogenetic tree was constructed using PhyElph software to study the evolutionary relationship between the three cichlid finfish species. The Phylogenetic or evolutionary relationship was established for the three fishes, Nile tilapia, GIFT, and Oscar cichlid, with the Phylogenetic tree. It was found that Nile tilapia and GIFT share a recent common ancestor, while Oscar cichlid does not share any evolutionary relationship with Nile tilapia and GIFT.

Research Progress in Plant Molecular Systematics of Lauraceae

Lauraceae is a large family of woody plants with high ecological and economic value. The tribal and generic division and phylogenetic relationship of Lauraceae have long been controversial. Based on morphological and molecular evidence, phylogenetic relationships within the Cinnamomeae, Laureae and Perseeae tribes, also called ‘the Core Lauraceae’, have arisen particular attention. In this review, we comprehensively collated the literatures on the phylogeny of Lauraceae published in recent years and summarized progress made in molecular systematic researches employing gene fragments, chloroplast genomes and DNA barcodings analyses. We clarified the phylogenetic relationships and main controversies of ‘the Core Lauraceae’, the systemic position of fuzzy genera (Neocinnamomum, Caryodaphnopsis and Cassytha) and the development of chloroplast genome and DNA barcodes. We further suggested and proposed the whole genome analysis and different inflorescence types would be possible to provide more information for further research on phylogenetic relationships and taxonomy of Lauraceae.

Hybridization and cryptic speciation in the Tropical Eastern Pacific octocoral genus Pacifigorgia

The shallow waters of the Tropical Eastern Pacific (TEP) harbor a species-rich octocoral fauna, with seven genera and 124 octocoral species described to date for the region. Of these lineages, Pacifigorgia, with 35 species, is by far the most speciose and abundant shallow-water octocoral occurring in the region. The speciation mechanisms resulting in this remarkable diversity remain speculative, despite the extensive taxonomic and molecular systematic research conducted so far in the TEP. Using genome-wide SNP markers, we provide evidence for hybridization and extensive cryptic speciation in Pacifigorgia, suggesting that the genus’ diversity has been underestimated by traditional and molecular systematic research. Our study highlights the difficulties faced by both traditional taxonomy and single-marker based molecular approaches to characterize octocoral diversity and evolution, and the role genome-wide molecular studies coupled to morphological research play to advance our understanding of this group.

Molecular systematic investigation of Philippine puddle frogs (Anura: Dicroglossidae: Occidozyga Kuhl and Van Hasselt, 1822) reveals new candidate species and a novel pattern of species dyads

Focusing on the phylogenetic relationships of puddle frog populations spanning the biogeographic interface between Sundaland (Borneo) and the Philippines, we demonstrate, for the first time, a widespread geographic pattern involving the existence of multiple divergent and co-distributed (sympatric) evolutionary lineages, most of which are not each other’s closest relatives, and all of which we interpret as probable distinct species. This pattern of co-occurrence in the form of pairs of ecologically distinct puddle frog forms (dyads), prevails throughout northern Borneo, Palawan, Tawi-Tawi, the Sulu Archipelago, and western Mindanao (Zamboanga). Previously obscured by outdated taxonomy and logistical, legal, and security obstacles to field-based natural history studies, this pattern has remained hidden from biogeographers and amphibian biologists by an uncontested proposal that Philippine Occidozyga laevis is a single, “widespread,” and “highly variable” species. In this paper we use an integrative synthesis of new genetic data, organismal phenotypic data, historical literature reports, and ecological observations to elucidate an interesting and potentially widespread pattern of puddle frog species coexistence at the Sundaland–Philippine biogeographic interface. Calling attention to this pattern opens promising possibilities for future research aimed at understanding the scope of this dyads pattern, and whether it extends to the more northern reaches of the Philippines. On either side of Huxley’s and Wallace’s lines, data suggest that the majority of puddle frog dyads at a given locality are not each other’s closest relatives (are more distantly related, or non-monophyletic) and, thus, assembled ecologically, likely coexisting now as a result of their ecological tendencies toward distinct microhabitats (warmer stagnant pools in open areas, versus cool, flowing streams enclosed in forest). If these pairs of species types are determined to be the geographic norm among the more isolated, central, and northern, Philippine faunas, an obvious question will be whether they have evolved into dual ecological forms, possibly in response to ecological opportunity and/or reduced competition. KEYWORDS: biogeography, taxonomy, microhabitat, cryptic species