Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life

DNA barcoding of passerine birds in Iran

Exploring genetic diversity is essential for precise species delimitation, especially within taxonomically complex groups like passerine birds. Traditional morphological methods often fail to resolve species boundaries; however, DNA barcoding, particularly through the mitochondrial cytochrome c oxidase subunit I (COI) gene, provides a powerful complementary method for accurate species identification. This study establishes a comprehensive DNA barcode library for Iranian passerine birds, analyzing 546 COI sequences from 94 species across 23 families and 53 genera. There is a pronounced barcode gap, with average intraspecific divergence at 0.41% and interspecific divergence at 18.6%. Notable intraspecific variation emerged in the Persian nuthatch (Sittatephronota) and the Lesser whitethroat (Currucacurruca), while the European goldfinch (Cardueliscarduelis) and the grey-crowned goldfinch (Cardueliscaniceps) showed limited genetic differentiation despite marked morphological distinctions. Phylogenetic analysis revealed significant east-west genetic splits in C.curruca and S.tephronota, reflecting Iran's geographic and zoogeographic boundaries. These findings demonstrate the effectiveness of DNA barcoding in elucidating biogeographic patterns, emphasizing Iran's key role as an ornithological crossroads for avian biodiversity. Moreover, our results suggest that much of the genetic variation in the COI gene arises from synonymous mutations, highlighting the role of purifying selection in shaping mtDNA diversity across species.

Effects of chronic metal exposure and metamorphosis on the microbiomes of larval and adult insects and riparian spiders through the aquatic-riparian food web

The macroinvertebrate microbiome controls various aspects of the host's physiology, from regulation of environmental contaminants to reproductive output. Aquatic insects provide critical nutritional subsidies linking aquatic and riparian food webs while simultaneously serving as a contaminant pathway for riparian insectivores in polluted ecosystems. Previous studies have characterized the transport and transfer of contaminants from aquatic to riparian ecosystems through insect metamorphosis, but both contaminant exposure and metamorphosis are energetically intensive processes that may cause host microbiomes to undergo radical transformation in structure and function, potentially affecting the host's physiology. We collected arthropods from three sites within Torch Lake, a historical copper mine in the Keweenaw Peninsula, Michigan, USA, and three sites within a nearby reference lake. Our objectives were to: 1) characterize the variation in microbiome communities and predicted metagenomic functions with legacy copper mining activity across space, among host types and family-level host taxonomy, 2) characterize how insect metamorphosis alters the microbiome community, including the degree of endosymbiotic infection, and predicted metagenomic function. We field-collected organisms, extracted their DNA, and sequenced the 16S region of the rRNA gene to characterize microbiome communities, then predicted metagenomic function. Site, lake, and host taxonomy affected the host microbiome community composition. Copper exposure increased the abundance of xenobiotic and lipid metabolism pathways in the Araneidae spider microbiome. Insect metamorphosis reduced the alpha diversity, altered the community composition, and predicted metagenomic function. We observed a bioconcentration of endosymbiotic bacteria in adult insects, especially holometabolous insects. Through metamorphosis, we observed a transition in function from xenobiotic degradation pathways to carbohydrate metabolism. Overall, contaminant exposure alters the microbiome composition in aquatic insects and riparian spiders and alters the function of the microbiome across the aquatic-riparian interface. Furthermore, metamorphosis is a critical element in shaping the aquatic insect microbiome across its life history.

Combination of Sample Preservation Approaches and DNA Extraction Methods for Long-Read Sequencing of Nudibranchs' Genomes

With the increasing interest in whole genome sequencing of eukaryotes, it is becoming evident that selecting the most suitable high molecular weight DNA extraction method is crucial for maximizing the benefits of long-read technologies. However, the DNA of many species cannot be processed immediately at the sampling site due to the remoteness of the location, necessitating tissue preservation that may affect DNA fragment size. This study aimed to identify the most suitable combination of four tissue preservation approaches and six DNA extraction methods to ensure high molecular weight DNA. A single Peltodoris atromaculata (Nudibranchia) specimen was sliced into ∼30 mg sub-samples, ensuring consistency across 24 preservation-extraction combinations processed in triplicates. Samples were either stored at 4°C, dried at room temperature, flash-frozen in liquid nitrogen, or preserved in ethanol and stored at -20°C. Afterward, they were processed using five commercially available kits specific for high molecular weight DNA extraction, as well as a custom DNA extraction protocol. Three aspects of DNA quality were evaluated: total yield, fragment size distribution, and availability of DNA for amplification. Most preservation-extraction combinations yielded optimal results in only some of the three DNA quality aspects. We identified six combinations suitable for long-read sequencing: a custom CTAB-based extraction protocol applied to frozen samples, Wizard (Promega) and Nanobind (PacBio) kits for both frozen and ethanol-preserved samples, and the ethanol preservation paired with Monarch (NEB) kits. The suitability of the six selected combinations was confirmed by PacBio sequencing, producing a total yield of 3.6 Gbp (3.2x estimated genome coverage). The results indicate that the success of high molecular weight DNA extractions is influenced by preservation methods. Although tested on nudibranchs, these findings are highly useful for genomic studies of other organisms, which may need to be preserved in remote locations before being transported to the laboratory for processing.

"Dark taxonomy": A new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment

We are entering the sixth mass extinction with little data for "dark taxa", although they comprise most species. Much of the neglect is due to the fact that conventional taxonomic methods struggle with handling thousands of specimens belonging to hundreds of species. We thus here propose a new strategy that we call "dark taxonomy". It addresses (i) taxonomic impediments, (ii) the lack of biodiversity baselines and (iii) the low impact of revisionary research. Taxonomic impediments are reduced by carrying out revisions at small geographic scales to keep the number of specimens low. The risk of taxonomic error is reduced by delimiting species based on two types of data. We furthermore show that dark taxonomy can yield important biodiversity baseline data by using samples obtained with biomonitoring traps. Lastly, we argue that the impact of revisionary research can be improved by publishing two papers addressing different readerships. The principles of dark taxonomy are illustrated by our taxonomic treatment of Singapore's fungus gnats (Mycetophilidae) based only on Malaise trap samples. We show that a first batch of specimens (N = 1454) contains 120 species, of which 115 are new to science, thus reducing taxonomic impediments by increasing the number of described Oriental species by 25%. Species delimitation started with using DNA barcodes to estimate the number of Molecular Operational Taxonomic Units (MOTUs) before "LIT" (Large-scale Integrative Taxonomy) was used to obtain the species boundaries for the 120 species by integrating morphological and molecular data. To test the taxonomic completeness of the revision, we next analysed a second batch of 1493 specimens and found that >97% belonged to the 120 species delimited based on the first batch. Indeed, the second batch only contained 18 new and rare MOTUs, i.e. our study suggests that a single revision can simultaneously yield the names for all important species and relevant biodiversity baseline data. Overall, we believe that "dark taxonomy" can quickly ready a large unknown taxon for biomonitoring.

Acanthocephalans as pollutant sinks? Higher pollutant accumulation in parasites may relieve their crustacean host

Increasing chemical pollution calls for a closer look at ecologically highly relevant host-parasite interactions to understand the persistence of organisms and populations in a polluted environment. The impact of chemical exposure within the host-parasite interactions - particularly the distinctive bioaccumulation behavior of organic micropollutants - can substantially influence the persistence of a species. This significance has been emphasized by previous research showing a higher tolerance of Gammarus roeselii (Amphipoda, Crustacea) infected with acanthocephalans during acute exposure to a pyrethroid. This suggests the presence of infection-related benefits within polluted environments. The present study addressed this complex relationship by investigating the chemical body burden and internal pollutant concentrations of both G. roeselii and its acanthocephalan parasites across a pollution gradient. Specifically, we analyzed 405 organic micropollutants and identified 123 of these in gammarids and their acanthocephalan parasites. Among the detected compounds, 22 are either banned or are no longer permitted for use in Germany. Remarkably, we discovered that the concentrations of pollutants were up to 35 times higher in the acanthocephalan parasites than in their crustacean intermediate hosts. The log KOW, the most frequently used measure of chemical hydrophobicity, could not explain the accumulation. Instead, the accumulation is likely explained by the unique physiology and high absorption capacity of acanthocephalans, combined with potentially limited biotransformation and excretion ability. This results in a redistribution of micropollutants within the host-parasite system, reducing the burden on the host up to 13.9 % and potentially explaining the observed helpful effects of parasitized G. roeselii in polluted environments. Our study underscores the often overlooked but significant role of host-parasite interactions in human-altered ecosystems, revealing how these relationships can mediate and amplify the impacts of micropollutants within aquatic communities. These insights stress the need to consider the pervasive influence of metazoan parasites in environmental assessments and pollution management strategies.

Barcode 100K Specimens: In a Single Nanopore Run

It is a global priority to better manage the biosphere, but action must be informed by comprehensive data on the abundance and distribution of species. The acquisition of such information is currently constrained by high costs. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive sequencing protocols are critical as the census of all animal species is likely to require the analysis of a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By enabling the sequencing of highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until recently, constrained adoption. However, the improved performance of its latest flow cells (R10.4.1) erases this barrier. This study demonstrates that a MinION flow cell can characterise an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow.

Unexpectedly complex distribution pattern of chestnut pest Niphades castanea Chao (Coleoptera: Curculionidae) based on mtDNA and ITS markers

Niphades castanea Chao (Coleoptera: Curculionidae), an important fruit insect pest of chestnuts (Castanea spp.), could cause chestnut involucre abscission ahead of time through larvae boring and feeding basal involucres, eventually causing huge economic losses. In this research, mitochondrial (COI and COII) and nuclear (ITS1) markers were used to investigate genetic variation among 15 different geographical populations of chestnut pest N castanea. The molecular diversity of N. castanea populations revealing three main phylogenetic clusters, with cluster I specifically distributed at high elevations in the western sampling points. Mitochondrial genes indicated population expansion events, and the ITS1 marker suggested a history of population expansion. Genetic diversity differentiation was significant among populations, indicating that geographical isolation impacts genetic differentiation among these places. AMOVA analyses confirmed substantial genetic differentiation between populations. Mantel correlogram analyses revealed a significant positive correlation between genetic differentiation and altitude/geographical distance at lower elevations and ranges, which reversed to a negative correlation at higher altitudes and ranges for all markers, indicating the role of altitude and geographical distance in shaping genetic diversity in N. castanea. This study contributes to a comprehensive understanding of the distribution, genetic diversity, and evolutionary history of N. castanea in the central of China, underscoring the impact of geographical factors on its genetic structure.

DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang

The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor-Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources.

Evolution of a biological thermocouple by adaptation of cytochrome c oxidase in a subterrestrial metazoan, Halicephalobus mephisto

In this study, we report a biological temperature-sensing electrical regulator in the cytochrome c oxidase of the Devil Worm, Halicephalobus mephisto. This extremophile metazoan was isolated 1.3 km underground in a South African goldmine, where it adapted to heat and potentially to hypoxia, making its mitochondrial sequence a likely target of adaptational change. We obtained the complete mitochondrial genome sequence of this organism and show through dN/dS analysis evidence of positive selection in H. mephisto cytochrome c oxidase subunits. Seventeen of these positively selected amino acid substitutions were located in proximity to the H- and K-pathway proton channels of the complex. Surprisingly, the H. mephisto cytochrome c oxidase completely shuts down at low temperatures (20 °C), leading to a 4.8-fold reduction in the transmembrane proton gradient (ΔΨm) compared to optimal temperature (37 °C). Direct measurement of oxygen consumption found a corresponding 4.6-fold drop at 20 °C compared to 37 °C. Correspondingly, the lifecycle of H. mephisto takes four times longer at low temperature than at higher. This elegant evolutionary adaptation creates a finely-tuned mitochondrial temperature sensor, allowing this ectothermic organism to maximize its reproductive success across varying environmental temperatures.

Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies

The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.

Molecular based identification and phylogenetic relationship of the leech Hirudinaria manillensis from India by using mitochondrial cytochrome c oxidase subunit I gene

BACKGROUND

A molecular approach for the identification of unknown species by the using mitochondrial cox1 gene is an effective and reliable as compared with morphological-based identification. Hirudinaria manillensis referred to as Asian Buffalo Leech, is found in South Asia and traditionally used as medicine owing to its medicinal properties.

METHODS AND RESULTS

The study aimed to isolate and identify the leech species using cox1 gene sequencing and their phylogenetic relationships. The nucleotide sequences of cytochrome c oxidase subunit I (cox1) mitochondrial genes were analyzed for species identification and the phylogenetic relationship of crucial therapeutic leech Hirudinaria manillensis. The isolated DNA from the leech sample was amplified with cox1 gene-specific primers. BLAST results with the H. manillensis sequence showed 89.24% homology with H. manillensis and phylogenetic tree analysis revealed the genetic relationship with other GenBank submitted sequences.

CONCLUSION

The present study concluded that the cox1 gene could be an effective way to identify the leech H. manillensis and provided sufficient phylogenetic information to distinguish H. manillensis indicating a significant mtDNA-based approach to species identification.

A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov

BACKGROUND

The geographic distribution and host-parasite interaction networks of Sarcocystis spp. in small mammals in eastern Asia remain incompletely known.

METHODS

Experimental infections, morphological and molecular characterizations were used for discrimination of a new Sarcocystis species isolated from colubrid snakes and small mammals collected in Thailand, Borneo and China.

RESULTS

We identified a new species, Sarcocystis muricoelognathis sp. nov., that features a relatively wide geographic distribution and infects both commensal and forest-inhabiting intermediate hosts. Sarcocystis sporocysts collected from rat snakes (Coelognathus radiatus, C. flavolineatus) in Thailand induced development of sarcocysts in experimental SD rats showing a type 10a cyst wall ultrastructure that was identical with those found in Rattus norvegicus from China and the forest rat Maxomys whiteheadi in Borneo. Its cystozoites had equal sizes in all intermediate hosts and locations, while sporocysts and cystozoites were distinct from other Sarcocystis species. Partial 28S rRNA sequences of S. muricoelognathis from M. whiteheadi were largely identical to those from R. norvegicus in China but distinct from newly sequenced Sarcocystis zuoi. The phylogeny of the nuclear 18S rRNA gene placed S. muricoelognathis within the so-called S. zuoi complex, including Sarcocystis attenuati, S. kani, S. scandentiborneensis and S. zuoi, while the latter clustered with the new species. However, the phylogeny of the ITS1-region confirmed the distinction between S. muricoelognathis and S. zuoi. Moreover, all three gene trees suggested that an isolate previously addressed as S. zuoi from Thailand (KU341120) is conspecific with S. muricoelognathis. Partial mitochondrial cox1 sequences of S. muricoelognathis were almost identical with those from other members of the group suggesting a shared, recent ancestry. Additionally, we isolated two partial 28S rRNA Sarcocystis sequences from Low's squirrel Sundasciurus lowii that clustered with those of S. scandentiborneensis from treeshews.

CONCLUSIONS

Our results provide strong evidence of broad geographic distributions of rodent-associated Sarcocystis and host shifts between commensal and forest small mammal species, even if the known host associations remain likely only snapshots of the true associations.

Molecular and morphological characterisation of larvae of the genus Diamesa Meigen, 1835 (Diptera: Chironomidae) in Alpine streams (Ötztal Alps, Austria)

Diamesa species (Diptera, Chironomidae) are widely distributed in freshwater ecosystems, and their life cycles are closely linked to environmental variables such as temperature, water quality, and sediment composition. Their sensitivity to environmental changes, particularly in response to pollution and habitat alterations, makes them valuable indicators of ecosystem health. The challenges associated with the morphological identification of larvae invoke the use of DNA barcoding for species determination. The mitochondrial cytochrome oxidase subunit I (COI) gene is regularly used for species identification but faces limitations, such as similar sequences in closely related species. To overcome this, we explored the use of the internal transcribed spacers (ITS) region in addition to COI for Diamesa larvae identification. Therefore, this study employs a combination of molecular markers alongside traditional morphological identification to enhance species discrimination. In total, 129 specimens were analysed, of which 101 were sampled from a glacier-fed stream in Rotmoostal, and the remaining 28 from spring-fed streams in the neighbouring valleys of Königstal and Timmelstal. This study reveals the inadequacy of utilizing single COI or ITS genes for comprehensive species differentiation within the genus Diamesa. However, the combined application of COI and ITS markers significantly enhances species identification resolution, surpassing the limitations faced by traditional taxonomists. Notably, this is evident in cases involving morphologically indistinguishable species, such as Diamesa latitarsis and Diamesa modesta. It highlights the potential of employing a multi-marker approach for more accurate and reliable Diamesa species identification. This method can be a powerful tool for identifying Diamesa species, shedding light on their remarkable adaptations to extreme environments and the impacts of environmental changes on their populations.

CRISPR-based diagnostics detects invasive insect pests

Rapid identification of organisms is essential for many biological and medical disciplines, from understanding basic ecosystem processes, disease diagnosis, to the detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than real-time PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a sophisticated laboratory, reduces the risk of cross-contamination, and can be completed in less than 1 h. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.

Evolution of a biological thermocouple by adaptation of cytochrome c oxidase in a subterrestrial metazoan

In this study we report a naturally evolved temperature-sensing electrical regulator in the cytochrome c oxidase of the Devil Worm, Halicephalobus mephisto. This extremophile metazoan was isolated 1.3 km underground in a South African goldmine, where it adapted to heat and potentially to hypoxia, making its mitochondrial sequence a likely target of adaptational change. We obtained the full mitochondrial genome sequence of this organism, and show through dN/dS analysis statistically robust evidence of positive selection in H. mephisto cytochrome c oxidase subunits. Seventeen of these positively-selected amino acid substitutions were localized in proximity to the H- and K-pathway proton channels of the complex. Surprisingly, the H. mephisto cytochrome c oxidase proton pump completely shuts down at low temperatures (20°C) leading to approximately a 4.8-fold reduction in the transmembrane proton gradient voltage (ΔΨm) compared to optimal temperature (37°C). Direct measurement of oxygen consumption found a corresponding 4.7-fold drop at 20°C compared to 37°C. Correspondingly, the lifecycle of H. mephisto takes four-fold longer at the low temperature compared to higher. This elegant evolutionary adaptation creates a finely-tuned mitochondrial temperature sensor, allowing this ectothermic organism to maximize its reproductive success in varying environmental temperatures. Our study shows that evolutionary innovation may remodel core metabolism to make it more accurately map onto environmental variation.

Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia

We investigated the morphology and phylogenetic relationships of novel and previously recognized Sarcocystis spp. infecting small mammals and colubrid snakes in Asia. The nuclear 18S rRNA and mitochondrial cox1 of Sarcocystis sp.1 from mangrove snakes (Boiga dendrophila) in Thailand and Sarcocystis sp.2 from a ricefield rat (Rattus argentiventer) in Sumatra were partially sequenced. Sporocysts of Sarcocystis sp.1 induced development of sarcocysts in experimentally infected rats, which showed a unique ultrastructure that was observed previously by S.P. Kan in rats from Malaysia; therefore, we describe this species as Sarcocystis kani sp. nov. Its integration into the 18S rRNA phylogeny of Sarcocystis spp. cycling between small mammals and colubrid snakes helped clarify relationships among the so-called S. zuoi-complex of molecularly cryptic species: Sarcocystis kani sp. nov., S. sp.2, S. attenuati, S. scandentiborneensis, and S. zuoi were all included in this clade. Tree topology was resolved into dichotomies congruent with the morphological disparities between the taxa. However, cox1 gene sequencing (including newly sequenced S. singaporensis and S. zamani) revealed that Sarcocystis kani, S. attenuati, and S. scandentiborneensis were identical suggesting a recent, common ancestry. To identify other distinctive features, lineage-specific molecular patterns within both genes were examined revealing that all 18S rRNA sequences of the S. zuoi - complex possess a unique, 7-nt long motif in helix 38 of domain V7 that was different in S. clethrionomyelaphis which branched off basally from the complex. Three-dimensional homology modelling of COX1 protein structure identified amino acid substitutions within the barcode area specific for the S. zuoi-complex and substantial divergence in structurally important amino acids between Sarcocystis species of snakes as definitive hosts and other lineages of the Sarcocystidae. We discuss the utility of selected genes for species delimitation of the Sarcocystis spp. under investigation, which probably evolved during recent radiations of their intermediate and definitive hosts.

Insights into the Diversity and Population Structure of Predominant Typhlocybinae Species Existing in Vineyards in Greece

Insects of the subfamily Typhlocybinae (Hemiptera: Cicadellidae) are pests of economically important agricultural and horticultural crops. They damage the plants directly or indirectly by transmitting plant pathogens, resulting in significant yield loss. Several leafhoppers of this subfamily use vines as hosts. Accurate and rapid identification is the key to their successful management. The aim of this study is to determine the Typhlocybinae species that exist in vineyards all over Greece and investigate the relationship between them. For this purpose, yellow sticky traps were placed, morphological and molecular data were collected, and phylogenetic models were analyzed. The mitochondrial marker Cytochrome Oxidase Subunit I (mtCOI) was applied for the DNA and phylogenetic analysis. The combination of morphological and molecular data resulted in identifying the existence of six different species all over Greece: Arboridia adanae, Asymmetrasca decedens, Hebata decipiens, Hebata vitis, Jacobiasca lybica and Zygina rhamni. Forty-eight different haplotypes were found to exist in the different regions of the country.

A Survey in Hawaii for Parasitoids of Citrus Whiteflies (Hemiptera: Aleyrodidae), for Introduction into Greece

Whitefly species of Aleurocanthus spiniferus (Quaintance) and A. woglumi Ashby (Hemiptera: Aleyrodidae) are serious pests of citrus and other important fruit crops. The problem of citrus has initiated the successful introduction of several natural enemies for biocontrol programs in Hawaii and many other countries. Here, we summarized the history of infestation and biocontrol efforts of the two whiteflies in Hawaii for possible parasitoid importation into Greece. Two Platygasteridae (Amitus hesperidum Silvestri, A. spiniferus (Brethes), and three Aphelinidae (Encarsia clypealis (Silvestri), E. smithi (Silvestri), E. perplexa Huang, and Polaszek) were released in Hawaii for biocontrol of the citrus whiteflies during the period 1974-1999. The aphelinid Cales noacki Howard, purposely released for Aleurothrixus flococcus (Maskell) in 1982, was also reported to attack other whiteflies, including Aleurocanthus species, on citrus. An additional aphelinid parasitoid, Encarsia nipponica Silvestri, native to Japan and China, was accidentally introduced and found to attack both citrus whiteflies on the islands. Since the colonization of introduced parasitoids in infested fields on four Hawaiian Islands, no survey has been conducted to evaluate their potential impact. We conducted two short surveys during September-November 2022 on the islands of Kauai, Hawaii, and Oahu to introduce the dominant parasitoids to Greece for the biocontrol of A. spiniferus. Results showed that the infestation level was very low on Kauai, Hawaii, and Oahu Islands, with a mean infestation level range of 1.4-3.1 on Hawaii and Oahu Islands, mostly on pummelo and sweet orange, with no detection on the island of Kauai. The dominant parasitoid was characterized as Encarsia perplexa, using molecular analysis. Its parasitism rates ranged from 0 to 28% on the island of Hawaii and 11 to 65% on the island of Oahu. Emerged parasitoids have been reared in Greece for evaluation. This was the first field survey of Hawaii since the introduction and release of citrus whitefly natural enemies.

A novel approach for the assessment of invertebrate behavior and its use in behavioral ecotoxicology

Sublethal effects are becoming more relevant in ecotoxicological test methods due to their higher sensitivity compared to lethal endpoints and their preventive nature. Such a promising sublethal endpoint is the movement behavior of invertebrates which is associated with the direct maintenance of various ecosystem processes, hence being of special interest for ecotoxicology. Disturbed movement behavior is often related to neurotoxicity and can affect drift, mate-finding, predator avoidance, and therefore population dynamics. We show the practical implementation of the ToxmateLab, a new device that allows monitoring the movement behavior of up to 48 organisms simultaneously, for behavioral ecotoxicology. We quantified behavioral reactions of Gammarus pulex (Amphipoda, Crustacea) after exposure to two pesticides (dichlorvos and methiocarb) and two pharmaceuticals (diazepam and ibuprofen) at sublethal, environmentally relevant concentrations. We simulated a short-term pulse contamination event that lasted 90 min. Within this short test period, we successfully identified behavioral patterns that were most pronounced upon exposure to the two pesticides: Methiocarb initially triggered hyperactivity, after which baseline behavior was restored. On the other hand, dichlorvos induced hypoactivity starting at a moderate concentration of 5 μg/L - a pattern we also found at the highest concentration of ibuprofen (10 μg/L). An additional acetylcholine esterase inhibition assay revealed no significant impact of the enzyme activity that would explain the altered movement behavior. This suggests that in environmentally realistic scenarios chemicals can induce stress - apart from mode-of-action - that affects non-target organisms' behavior. Overall, our study proves the practical applicability of empirical behavioral ecotoxicological approaches and thus represents a next step towards routine practical use.

Influence of substitution model selection on protein phylogenetic tree reconstruction

Probabilistic phylogenetic tree reconstruction is traditionally performed under a best-fitting substitution model of molecular evolution previously selected according to diverse statistical criteria. Interestingly, some recent studies proposed that this procedure is unnecessary for phylogenetic tree reconstruction leading to a debate in the field. In contrast to DNA sequences, phylogenetic tree reconstruction from protein sequences is traditionally based on empirical exchangeability matrices that can differ among taxonomic groups and protein families. Considering this aspect, here we investigated the influence of selecting a substitution model of protein evolution on phylogenetic tree reconstruction by the analyses of real and simulated data. We found that phylogenetic tree reconstructions based on a selected best-fitting substitution model of protein evolution are the most accurate, in terms of topology and branch lengths, compared with those derived from substitution models with amino acid replacement matrices far from the selected best-fitting model, especially when the data has large genetic diversity. Indeed, we found that substitution models with similar amino acid replacement matrices produce similar reconstructed phylogenetic trees, suggesting the use of substitution models as similar as possible to a selected best-fitting model when the latter cannot be used. Therefore, we recommend the use of the traditional protocol of selection among substitution models of evolution for protein phylogenetic tree reconstruction.

CRISPR-based diagnostics detects invasive insect pests

Rapid identification of organisms is essential across many biological and medical disciplines, from understanding basic ecosystem processes and how organisms respond to environmental change, to disease diagnosis and detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta, and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than other real time-PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a lab setting, reduces the risk of cross-contamination, and can be completed in less than one hour. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.

Mordellistena platypoda, a new species of tumbling flower beetle from the island of Ischia in Italy (Coleoptera, Mordellidae)

Mordellistena A. Costa, 1854, the most species-rich genus of tumbling flower beetles comprises more than 800 species worldwide and more than 150 reported from Europe. Here, a new species Mordellistena (s. str.) platypoda is described from the island of Ischia in Italy. The species hypothesis is based primarily on morphological characters which are visualised using scanning electron microscopy images, high-resolution photographs, and drawings. The species hypothesis is supported by analysis of a 658 bp fragment of cytochrome c oxidase subunit I (COI). Divergences in the COI gene are evaluated using maximum likelihood and Bayesian inference analyses. The species delimitation is assessed using Assemble Species by Automatic Partitioning (ASAP) and Poisson Tree Processes (PTP) methods. Genetic distances are visualised using multidimensional scaling. Mordellistena platypoda Selnekovič, Goffová & Kodada, sp. nov. is recovered as a well-separated species by both molecular and morphological analyses. Our results show that M. platypoda Selnekovič, Goffová & Kodada, sp. nov. is most closely related to M. tarsata Mulsant, 1856, although the two species differ significantly in vestiture colouration, presence of lateral ctenidia on the third metatarsomere, and presence of sexual dimorphism on the protibia. The results indicate that such morphological differences, which were traditionally used to distinguish between species groups, may in fact be present between closely related species. Interestingly, examination of the numerous museum material did not reveal additional specimens of the new species, and therefore M. platypoda Selnekovič, Goffová & Kodada, sp. nov. is currently known only from the Italian island of Ischia.

Can metabolic traits explain animal community assembly and functioning?

All animals on Earth compete for free energy, which is acquired, assimilated, and ultimately allocated to growth and reproduction. Competition is strongest within communities of sympatric, ecologically similar animals of roughly equal size (i.e. horizontal communities), which are often the focus of traditional community ecology. The replacement of taxonomic identities with functional traits has improved our ability to decipher the ecological dynamics that govern the assembly and functioning of animal communities. Yet, the use of low-resolution and taxonomically idiosyncratic traits in animals may have hampered progress to date. An animal's metabolic rate (MR) determines the costs of basic organismal processes and activities, thus linking major aspects of the multifaceted constructs of ecological niches (where, when, and how energy is obtained) and ecological fitness (how much energy is accumulated and passed on to future generations). We review evidence from organismal physiology to large-scale analyses across the tree of life to propose that MR gives rise to a group of meaningful functional traits - resting metabolic rate (RMR), maximum metabolic rate (MMR), and aerobic scope (AS) - that may permit an improved quantification of the energetic basis of species coexistence and, ultimately, the assembly and functioning of animal communities. Specifically, metabolic traits integrate across a variety of typical trait proxies for energy acquisition and allocation in animals (e.g. body size, diet, mobility, life history, habitat use), to yield a smaller suite of continuous quantities that: (1) can be precisely measured for individuals in a standardized fashion; and (2) apply to all animals regardless of their body plan, habitat, or taxonomic affiliation. While integrating metabolic traits into animal community ecology is neither a panacea to disentangling the nuanced effects of biological differences on animal community structure and functioning, nor without challenges, a small number of studies across different taxa suggest that MR may serve as a useful proxy for the energetic basis of competition in animals. Thus, the application of MR traits for animal communities can lead to a more general understanding of community assembly and functioning, enhance our ability to trace eco-evolutionary dynamics from genotypes to phenotypes (and vice versa), and help predict the responses of animal communities to environmental change. While trait-based ecology has improved our knowledge of animal communities to date, a more explicit energetic lens via the integration of metabolic traits may further strengthen the existing framework.

VLF: An R package for the analysis of very low frequency variants in DNA sequences

Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.

Genetic diversity of tick (Acari: Ixodidae) populations and molecular detection of Anaplasma and Ehrlichia infesting beef cattle from upper-northeastern Thailand

Genetic diversity, genetic structure and demographic history of the ticks infesting beef cattle in Thailand were examined based on mitochondrial cytochrome c oxidase I (cox1) sequences. Tick samples were collected in 12 provinces in upper-northeastern Thailand. Three species were found; Rhipicephalus microplus, R. sanguineus, and Haemaphysalis bispinosa. Of these, R. microplus was by far the most abundant species in beef cattle and was widely distributed throughout the area. No cox1 sequence variation was found in the R. sanguineus or H. bispinosa specimens collected. Low nucleotide diversity but high haplotype diversity was observed in R. microplus. All collected R. microplus specimens belonged to lineage A. Mismatch-distribution analysis, as well as Tajima's D and Fu's Fs tests, provided evidence of recent demographic expansion. A subsample of tick specimens was investigated for presence of Anaplasma and Ehrlichia using a fragment of the 16S rRNA gene. Three species of Anaplasma were detected from R. microplus; Anaplasma marginale (19.08%), Anaplasma platys (1.97%) and unidentified Anaplasma strain (0.66%). The infection rate of Ehrlichia was 7.24% (two ticks were infected with E. minasensis (1.97%) and eight with an unidentified Ehrlichia strain (5.26%). No infections were found in R. sanguineus or H. bispinosa. This is the first report of A. platys and E. minasensis in cattle ticks in Thailand, providing information for future epidemiological surveys and control strategies in this region.

Structure and molecular evolution of the barcode fragment of cytochrome oxidase I (COI) in Macrocheles (Acari: Mesostigmata: Macrochelidae)

Consisting of approximately 320 species, Macrocheles is the most widely distributed genus in the family Macrochelidae. Though some studies have focused on the description of Macrochelidae using molecular techniques (e.g., RAPD) and sequencing of some genes, the interspecies relationships within Macrocheles still remain uncertain. As such, in the present study, we examine all publicly available data in GenBank to explore the evolutionary relationships, divergence times, and amino acid variations within Macrocheles. Exploring the patterns of variation in the secondary protein structure shows high levels of conservation in the second and last helices, emphasizing their involvement in the energy metabolism function of the cytochrome oxidase subunit I enzyme. According to our phylogenetic analysis, all available Macrocheles species are clustered in a monophyletic group. However, in the reconstructed trees, we subdivided M. merdarius and M. willowae into two well-supported intraspecific clades that are driven by geographic separation and host specificity. We also estimate the divergence time of selected species using calibration evidence from available fossils and previous studies. Thus, we estimate that the age of the Parasitiformes is 320.4 (273.3-384.3) Mya (Permian), and the Mesostigmata is 285.1 (270.8-286.4) Mya (Carboniferous), both with likely origins in the Paleozoic era. We also estimate that Macrocheles diverged from other Mesostigmata mites during the Mesozoic, approximately 222.9 Mya.

Exploring the Biodiversity of a European NATURA 2000 Mediterranean Lagoon through eDNA Metabarcoding

Coastal lagoons are considered important habitats both for ecological functions and biodiversity worldwide. Thus, they provide relevant ecosystem services and valuable natural resources. However, coastal lagoons are highly susceptible to anthropogenic pressures that can cause biodiversity losses and require specific biomonitoring programs as well as management measures. In this research, we applied environmental DNA (eDNA) metabarcoding to investigate the biodiversity of a poorly known Mediterranean lagoon included in the European Natura 2000 Network. We used the cytochrome oxidase I (COI) gene marker to capture the entire biodiversity of this highly diversified aquatic coastal environment. With a low sampling effort and rapid laboratory practices, a large amount of valuable biodiversity data was generated and analyzed. Interestingly, this straightforward and broad molecular surveying of biodiversity unveiled a wide variety of taxonomic groups, such as benthic macroinvertebrates, zooplankton, phytoplankton, and macroalgae, which are frequently used as ecological indicators. We were able to detect species that were previously morphologically identified, as well as species never identified before. This research underlines the validity of eDNA metabarcoding in assessing the biodiversity in a poorly known and protected Mediterranean lagoon ecosystem, as well as in identifying the early warnings of environmental stressors. Finally, the research highlights the need to investigate multiple target genes and primers set for a larger analysis of specific species.

Polymorphisms in the hypervariable control region of the mitochondrial DNA differentiate BPH populations

The brown planthopper (BPH; Nilaparvata lugens) is one of India's most destructive pests of rice. BPH, a monophagous migratory insect, reported from all major rice-growing ecosystems of the country, is capable of traversing large distances and causing massive crop loss. A crucial step for developing viable management strategies is understanding its population dynamics. Very few reliable markers are currently available to screen BPH populations for their diversity. In the current investigation, we developed a combinatorial approach using the polymorphism present within the mitochondrial Control Region of BPH and in the nuclear genome (genomic simple sequence repeats; gSSRs) to unravel the diversity present in BPH populations collected from various rice-growing regions of India. Using two specific primer pairs, the complete Control Region (1112 to 2612 bp) was PCR amplified as two overlapping fragments, cloned and sequenced from BPH individuals representing nine different populations. Results revealed extensive polymorphism within this region due to a variable number of tandem repeats. The three selected gSSR markers also exhibited population-specific amplification patterns. Overall genetic diversity between the nine populations was high (>5%). Further, in silico double-digestion of the consensus sequences of the Control Region, with HpyCH4IV and Tsp45I restriction enzymes, revealed unique restriction fragment length polymorphisms (digital-RFLPs; dRFLPs) that differentiated all the nine BPH populations. To the best of our knowledge, this is the first report of markers developed from the Control Region of the BPH mitogenome that can differentiate populations. Eventually, such reliable and rapid marker-based identification of BPH populations will pave the way for an efficient pest management strategy.

Luminescent characteristics and mitochondrial COI barcodes of nine cohabitated Taiwanese fireflies

Background

Over 50 Taiwanese firefly species have been discovered, but scientists lack information regarding most of their genetics, bioluminescent features, and cohabitating phenomena. In this study, we focus on morphological species identification and phylogeny reconstructed by COI barcoding, as well as luminescent characteristics of cohabited Taiwanese firefly species to determine the key factors that influenced how distinct bioluminescent species evolved to coexist and proliferate within the same habitat.

Methods

In this study, 366 specimens from nine species were collected in northern Taiwan from April to August, 2016-2019. First, the species and sex of the specimens were morphologically and genetically identified. Then, their luminescent spectra and intensities were recorded using a spectrometer and a power meter, respectively. The habitat temperature, relative humidity, and environmental light intensity were also measured. The cytochrome oxidase I (COI) gene sequence was used as a DNA barcode to reveal the phylogenetic relationships of cohabitated species.

Results

Nine species-eight adult species (Abscondita chinensis, Abscondita cerata, Aquatica ficta, Luciola curtithorax, Luciola kagiana, Luciola filiformis, Curtos sauteri, and Curtos costipennis) and one larval Pyrocoelia praetexta-were morphologically identified. The nine species could be found in April-August. Six of the eight adult species shared an overlap occurrence period in May. Luminescent spectra analysis revealed that the λ _max of studied species ranged from 552-572 nm (yellow-green to orange-yellow). The average luminescent intensity range of these species was about 1.2-14 lux (182.1-2,048 nW/cm²) for males and 0.8-5.8 lux (122.8-850 nW/cm²) for females, and the maximum luminescent intensity of males was 1.01-7.26-fold higher than that of females. Compared with previous studies, this study demonstrates that different λ _max, species-specific flash patterns, microhabitat choices, nocturnal activity time, and/or an isolated mating season are key factors that may lead to the species-specific courtship of cohabitated fireflies. Moreover, we estimated that the fireflies start flashing or flying when the environmental light intensity decreased to 6.49-28.1 lux. Thus, based on a rough theoretical calculation, the sensing distance between male and female fireflies might be 1.8-2.7 m apart in the dark. In addition, the mitochondrial COI barcode identified species with high resolution and suggested that most of the studied species have been placed correctly with congeners in previous phylogenies. Several cryptic species were revealed by the COI barcode with 3.27%-12.3% variation. This study renews the idea that fireflies' luminescence color originated from the green color of a Lampyridae ancestor, then red-shifted to yellow-green in Luciolinae, and further changed to orange-yellow color in some derived species.

Drivers for mutation in amino acid sequences of two mitochondrial proteins (Cytb and COI) in Phytoseiidae mites (Acari: Mesostigmata)

Mutations in amino acid sequences can affect protein function. Such aspects have been poorly studied for arthropods. As recent studies have shown mutations in cytochrome b (Cytb) associated with geographic locations in several Phytoseiidae species, the present study aims at investigating (i) the mutation pattern in additional species for the Cytb fragment, (ii) the mutation pattern for another mitochondrial amino acid sequence, cytochrome c oxidase subunit 1 (COI), and (iii) factors affecting the mutations observed (taxonomy, plant support, climatic variables, wild vs. commercialised species). Mutations in amino acid sequences were assessed in seven Phytoseiidae species, with populations collected in contrasted environments. The DNA sequences were mainly obtained from published studies and some were newly obtained. Mutations were observed within and between the populations considered for both fragments, with higher mutation rates in Cytb than in COI sequences, confirming the robustness of this former fragment. Plant support and taxonomic position were not related to mutation patterns. A lower number of mutations was observed in commercialised populations than in wild ones. As preliminary tendencies, mutations in Cytb and COI sequences seem associated to temperature and moisture. Such a preliminary approach, attempting to relate mutation to functional adaptations, clearly opens new research tracks for better assessment of the drivers of mite adaptation, in a context of climate change.

Molecular characterization and phylogenetic relationships among Rhynchophorus sp. haplotypes in Makkah Al-Mukarramah Region-KSA

The study aims at detecting and characterizing haplotypes of red palm weevil (RPW) Rhynchophorus sp. in the Western region of Saudi Arabia based on the cytochrome oxidase subunit I (COI) gene sequence. The results indicated the occurrence of 17 nucleotide substitutions, of which three were nonsynonymous (NS). These three NS substitutions resulted in the variation in amino acid sequence in three positions, out of 133. These amino acids are isoleucine/valine, glycine/serine, and arginine/histidine. Based on the chemical properties of the cytochrome C oxidase (COX) enzyme, it is likely that the change at the first position has no effect, while changes at the other two positions can affect the chemical properties of the enzyme. At the three-dimensional (3D) level, the first two positions exist at the border or inside loop 3–4 of the enzyme, while the third position exists inside loop 4–5. These two loops influence the folding pattern of the enzyme, thus, likely affecting the function of the enzyme. However, it is unlikely that variations in the three positions will affect the binding ability of the heme group, which promotes the action of the COX enzyme in the electron transport chain. Variations in chemical properties and 3D structure of COX enzyme might be an evolutionary process (positive selection) that promotes in-time and in-site adaptation to the insect. In conclusion, this study can be helpful in pest management programs and in tracing RPW geographic spread and migration in Saudi Arabia.

ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data

Viruses are ubiquitous in humans and various environments and continually mutate themselves. Identifying viruses in an environment without cultivation is challenging; however, promoting the screening of novel viruses and expanding the knowledge of viral space is essential. Homology-based methods that identify viruses using known viral genomes rely on sequence alignments, making it difficult to capture remote homologs of the known viruses. To accurately capture viral signals from metagenomic samples, models are needed to understand the patterns encoded in the viral genomes. In this study, we developed a hierarchical BERT model named ViBE to detect eukaryotic viruses from metagenome sequencing data and classify them at the order level. We pre-trained ViBE using read-like sequences generated from the virus reference genomes and derived three fine-tuned models that classify paired-end reads to orders for eukaryotic deoxyribonucleic acid viruses and eukaryotic ribonucleic acid viruses. ViBE achieved higher recall than state-of-the-art alignment-based methods while maintaining comparable precision. ViBE outperformed state-of-the-art alignment-free methods for all test cases. The performance of ViBE was also verified using real sequencing datasets, including the vaginal virome.

Vast Gene Flow among the Spanish Populations of the Pest Bactrocera oleae (Diptera, Tephritidae), Phylogeography of a Metapopulation to Be Controlled and Its Mediterranean Genetic Context

Simple Summary

The output of olive industry at the Mediterranean Basin, headed by Spain, is huge worldwide. The olive fruit fly Bactrocera oleae is the major pest of olive orchards. The damages it causes become in considerable economic losses as well as a decrease in oil quantity and quality. A key question for the success of pest control strategies is the further knowledge about the species, and genetic data becomes essential for this purpose. The present work analyses more than 250 fruit flies from six different Mediterranean countries, showing relevant data about the genetic structure and gene flow of this damaging pest. These findings are helpful to improve the integrated pest management strategies according to the current European Guidelines.

Abstract

Spain is the leading producer of olives and olive oil. Ninety-five percent of world production originate from Spain and other regions of the Mediterranean Basin. However, these olive-growing countries face a major problem, the harmful fly Bactrocera oleae, the main pest of olive crops. To improve its control, one of the challenges is the further knowledge of the species and populations dynamics in this area. A phylogeographic work is necessary to further characterise the levels and distribution patterns of genetic diversity of the Spanish populations and their genetic relationships with other Mediterranean populations. A 1151 bp fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene has been analysed in over 250 specimens of the six main Mediterranean countries via sequencing. Genetic diversity parameters were high; 51 new haplotypes have been identified showing a geographical pattern across the Mediterranean area. The data revealed that olive fruit fly populations have been long time established in the Mediterranean Basin with two genetic groups. Gene flow seems to be the main process in shaping this genetic structure as well as fly’s colonisation routes that have paralleled those of the olive tree.

Coconut Rhinoceros Beetle in Samoa: Review of a Century-Old Invasion and Prospects for Control in a Changing Future

Simple Summary

Coconut rhinoceros beetle (CRB) is one of the major pests of coconut and oil palms in the Asia-Pacific region. Since its accidental introduction in Samoa in 1909, the invasive CRB has spread to several countries and territories within the Pacific and Indian Oceans, severely damaging coconut palms and affecting peoples’ livelihoods. In the 100 years since CRB established on Samoa, it remains the primary pest on the island with periods of heavy damage when integrated pest management (IPM) breaks down. The Samoan case is an excellent example of implementing biocontrol and IPM in a dynamic Pacific environment. As society and the economics of production in Samoa have changed, the level of control has varied, with recent concern about surges of the pest. The review synthesizes historical lessons and provide recommendations on how to protect coconut palms in the changing environment of Samoa which are also applicable for protection of palms in the wider Asia/Pacific region.

Abstract

It is now more than 100 years since the coconut rhinoceros beetle (CRB: Oryctes rhinoceros L.) was first detected in the Pacific Island state of Samoa. The exotic pest from Asia became the principal pest of coconut palms in Samoa and, from this first point of invasion, spread to several surrounding countries in the South-West Pacific Ocean. An intensive control operation was initiated, but the beetle could not be eliminated. Various pest management strategies were attempted but had limited success until the introduction of a biological control agent (BCA), Oryctes rhinoceros nudivirus (OrNV), during the late 1960s and early 1970s. The biocontrol release was very successful and became the prime example of “classical biological control” of an insect pest by a virus. Changing economic and social conditions in Samoa and other islands of the Pacific require a re-evaluation of the threat of CRB to coconut production to suggest how the IPM system may be modified to meet future needs. Therefore, it is timely to review the history of CRB in Samoa and summarize experiences in development of an integrated pest management (IPM) system limiting the impact of the pest. We also present results from a recent study conducted in 2020 on the island of Upolu to define the current status of the CRB population and its BCA, OrNV. The lessons from Samoa, with its long history of containment and management of CRB, are applicable to more recent invasion sites. Recommendations are provided to modify the IPM programme to enhance the sustainable control of CRB and support the ongoing coconut replantation program promoted by the Samoan government.

Towards Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa

New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling “dark taxa,” here defined as groups for which \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$<$\end{document}10\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} of all species are described and the estimated diversity exceeds 1,000 species. Species delimitation for these taxa should be based on multiple data sources (“integrative taxonomy”) but collecting multiple types of data risks impeding a discovery process that is already too slow. We here develop large-scale integrative taxonomy (LIT), an explicit method where preliminary species hypotheses are generated based on inexpensive data that can be obtained quickly and cost-effectively. These hypotheses are then evaluated based on a more expensive type of “validation data” that is only obtained for specimens selected based on objective criteria applied to the preliminary species hypotheses. We here use this approach to sort 18,000 scuttle flies (Diptera: Phoridae) into 315 preliminary species hypotheses based on next-generation sequencing barcode (313 bp) clusters (using objective clustering [OC] with a 3\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} threshold). These clusters are then evaluated with morphology as the validation data. We develop quantitative indicators for predicting which barcode clusters are likely to be incongruent with morphospecies by randomly selecting 100 clusters for in-depth validation with morphology. A linear model demonstrates that the best predictors for incongruence between barcode clusters and morphology are maximum p-distance within the cluster and a newly proposed index that measures cluster stability across different clustering thresholds. A test of these indicators using the 215 remaining clusters reveals that these predictors correctly identify all clusters that are incongruent with morphology. In our study, all morphospecies are true or disjoint subsets of the initial barcode clusters so that all incongruence can be eliminated by varying clustering thresholds. This leads to a discussion of when a third data source is needed to resolve incongruent grouping statements. The morphological validation step in our study involved 1,039 specimens (5.8\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} of the total). The formal LIT protocol we propose would only have required the study of 915 (5.1\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document}: 2.5 specimens per species), as we show that clusters without signatures of incongruence can be validated by only studying two specimens representing the most divergent haplotypes. To test the generality of our results across different barcode clustering techniques, we establish that the levels of incongruence are similar across OC, Automatic Barcode Gap Discovery (ABGD), Poisson Tree Processes (PTP), and Refined Single Linkage (RESL) (used by Barcode of Life Data System to assign Barcode Index Numbers [BINs]). OC and ABGD achieved a maximum congruence score with the morphology of 89\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} while PTP was slightly less effective (84\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document}). RESL could only be tested for a subset of the specimens because the algorithm is not public. BINs based on 277 of the original 1,714 haplotypes were 86\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} congruent with morphology while the values were 89\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} for OC, 74\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} for PTP, and 72\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\%$\end{document} for ABGD. [Biodiversity discovery; dark taxa; DNA barcodes; integrative taxonomy.]

Host phylogeny, habitat, and diet are main drivers of the cephalopod and mollusk gut microbiome

Background

Invertebrates are a very attractive subject for studying host-microbe interactions because of their simple gut microbial community and host diversity. Studying the composition of invertebrate gut microbiota and the determining factors is essential for understanding their symbiotic mechanism. Cephalopods are invertebrates that have similar biological properties to vertebrates such as closed circulation system, an advanced nervous system, and a well-differentiated digestive system. However, it is not currently known whether their microbiomes have more in common with vertebrates or invertebrates. This study reports on the microbial composition of six cephalopod species and compares them with other mollusk and marine fish microbiomes to investigate the factors that shape the gut microbiota.

Results

Each cephalopod gut consisted of a distinct consortium of microbes, with Photobacterium and Mycoplasma identified as core taxa. The gut microbial composition of cephalopod reflected their host phylogeny, the importance of which was supported by a detailed oligotype-level analysis of operational taxonomic units assigned to Photobacterium and Mycoplasma. Photobacterium typically inhabited multiple hosts, whereas Mycoplasma tended to show host-specific colonization. Furthermore, we showed that class Cephalopoda has a distinct gut microbial community from those of other mollusk groups or marine fish. We also showed that the gut microbiota of phylum Mollusca was determined by host phylogeny, habitat, and diet.

Conclusion

We have provided the first comparative analysis of cephalopod and mollusk gut microbial communities. The gut microbial community of cephalopods is composed of distinctive microbes and is strongly associated with their phylogeny. The Photobacterium and Mycoplasma genera are core taxa within the cephalopod gut microbiota. Collectively, our findings provide evidence that cephalopod and mollusk gut microbiomes reflect host phylogeny, habitat, and diet. It is hoped that these data can contribute to future studies on invertebrate–microbe interactions.

Widely used, short 16S rRNA mitochondrial gene fragments yield poor and erratic results in phylogenetic estimation and species delimitation of amphibians

Background

The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is more commonly used in other animal groups. However, studies employ different primer combinations that target different lengths/regions of the 16S gene ranging from complete gene sequences (~ 1500 bp) to short fragments (~ 500 bp), the latter of which is the most ubiquitously used. Sequences of different lengths are often concatenated, compared, and/or jointly analyzed to infer phylogenetic relationships, estimate genetic divergence (p-distances), and justify the recognition of new species (species delimitation), making the 16S gene region, by far, the most influential molecular marker in amphibian systematics. Despite their ubiquitous and multifarious use, no studies have ever been conducted to evaluate the congruence and performance among the different fragment lengths.

Results

Using empirical data derived from both Sanger-based and genomic approaches, we show that full-length 16S sequences recover the most accurate phylogenetic relationships, highest branch support, lowest variation in genetic distances (pairwise p-distances), and best-scoring species delimitation partitions. In contrast, widely used short fragments produce inaccurate phylogenetic reconstructions, lower and more variable branch support, erratic genetic distances, and low-scoring species delimitation partitions, the numbers of which are vastly overestimated. The relatively poor performance of short 16S fragments is likely due to insufficient phylogenetic information content.

Conclusions

Taken together, our results demonstrate that short 16S fragments are unable to match the efficacy achieved by full-length sequences in terms of topological accuracy, heuristic branch support, genetic divergences, and species delimitation partitions, and thus, phylogenetic and taxonomic inferences that are predicated on short 16S fragments should be interpreted with caution. However, short 16S fragments can still be useful for species identification, rapid assessments, or definitively coupling complex life stages in natural history studies and faunal inventories. While the full 16S sequence performs best, it requires the use of several primer pairs that increases cost, time, and effort. As a compromise, our results demonstrate that practitioners should utilize medium-length primers in favor of the short-fragment primers because they have the potential to markedly improve phylogenetic inference and species delimitation without additional cost.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01994-y.

Phyllidiidae (Nudibranchia, Heterobranchia, Gastropoda): an integrative taxonomic approach including chemical analyses

Members of the widely distributed and common nudibranch family Phyllidiidae are often easily spotted in the marine environment because of their conspicuous colours and obvious presence on the reef. They are interesting with regard to their defensive chemical compounds that may lead to new drug discoveries. Despite their abundance, the family is also well known for its taxonomic problems and the difficulties in species identification due to very similarly coloured species and lack of morphological characters. In this study, phyllidiid species were analysed using an integrative approach. Molecular analysis of the mitochondrial genes 16S and CO1 was utilised, running phylogenetic analyses, species delimitation tests, and haplotype network analyses. Additionally, for the first time, external morphological characters were analysed, museum material was re-analysed, and chemical profiles were applied for characterising species. The analyses are based on sequences of 598 specimens collected in Indonesia by the team, with the addition of published sequences available on GenBank. This study comprises 11 species of Phyllidia, seven species of Phyllidiopsis, and at least 14 species of Phyllidiella. Moreover, 11 species belonging to these three genera are probably new to science, Phyllidiopsis pipeki is synonymised with P. krempfi, and Phyllidiella albonigra is resurrected. Some of the external colouration previously used for species identification is shown to not be valid, but alternative characters are provided for most species. Chemical analyses led to species characterisation in a few examples, indicating that these species use particular sponge species as food; however, many species show a broad array of compounds and are therefore characterised more by their composition or profile than by distinct or unique compounds.

Lemnaceae and Orontiaceae Are Phylogenetically and Morphologically Distinct from Araceae

Duckweeds comprise a distinctive clade of pleustophytic monocots that traditionally has been classified as the family Lemnaceae. However, molecular evidence has called into question their phylogenetic independence, with some authors asserting instead that duckweeds should be reclassified as subfamily Lemnoideae of an expanded family Araceae. Although a close phylogenetic relationship of duckweeds with traditional Araceae has been supported by multiple studies, the taxonomic disposition of duckweeds must be evaluated more critically to promote nomenclatural stability and utility. Subsuming duckweeds as a morphologically incongruent lineage of Araceae effectively eliminates the family category of Lemnaceae that has been widely used for many years. Instead, we suggest that Araceae subfamily Orontioideae should be restored to family status as Orontiaceae, which thereby would enable the recognition of three morphologically and phylogenetically distinct lineages: Araceae, Lemnaceae, and Orontiaceae.

Volatiles Emission by Crotalaria nitens after Insect Attack

Plants are known to increase the emission of volatile organic compounds upon the damage of phytophagous insects. However, very little is known about the composition and temporal dynamics of volatiles released by wild plants of the genus Crotalaria (Fabaceae) attacked with the specialist lepidopteran caterpillar Utetheisa ornatrix (Linnaeus) (Erebidae). In this work, the herbivore-induced plant volatiles (HIPV) emitted by Crotalaria nitens Kunth plants were isolated with solid phase micro-extraction and the conventional purge and trap technique, and their identification was carried out by GC/MS. The poly-dimethylsiloxane/divinylbenzene fiber showed higher affinity for the extraction of apolar compounds (e.g., trans-β-caryophyllene) compared to the Porapak™-Q adsorbent from the purge & trap method that extracted more polar compounds (e.g., trans-nerolidol and indole). The compounds emitted by C. nitens were mainly green leaf volatile substances, terpenoids, aromatics, and aldoximes (isobutyraldoxime and 2-methylbutyraldoxime), whose maximum emission was six hours after the attack. The attack by caterpillars significantly increased the volatile compounds emission in the C. nitens leaves compared to those subjected to mechanical damage. This result indicated that the U. ornatrix caterpillar is responsible for generating a specific response in C. nitens plants. It was demonstrated that HIPVs repelled conspecific moths from attacked plants and favored oviposition in those without damage. The results showed the importance of volatiles in plant-insect interactions, as well as the choice of appropriate extraction and analytical methods for their study.

Multi-locus phylogenetic analyses uncover species boundaries and reveal the occurrence of two new entomopathogenic nematode species, Heterorhabditis ruandica n. sp. and Heterorhabditis zacatecana n. sp

Species of the nematode genus Heterorhabditis are important biological control agents against agricultural pests. The taxonomy of this group is still unclear as it currently relies on phylogenetic reconstructions based on a few genetic markers with little resolutive power, specially of closely related species. To fill this knowledge gap, we sequenced several phylogenetically relevant genetic loci and used them to reconstruct phylogenetic trees, to calculate sequence similarity scores, and to determine signatures of species- and population-specific genetic polymorphism. In addition, we revisited the current literature related to the description, synonymisation, and declaration as species inquirendae of Heterorhabditis species to compile taxonomically relevant morphological and morphometric characters, characterized new nematode isolates at the morphological and morphometrical level, and conducted self-crossing and cross-hybridization experiments. The results of this study show that the sequences of the mitochondrial cytochrome C oxidase subunit I (COI) gene provide better phylogenetic resolutive power than the sequences of nuclear rRNA genes and that this gene marker can phylogenetically resolve closely related species and even populations of the same species with high precision. Using this gene marker, we found two new species, Heterorhabditis ruandica n. sp. and Heterorhabditis zacatecana n. sp. A detailed characterization of these species at the morphological and morphometric levels and nematode reproduction assays revealed that the threshold for species delimitation in this genus, using COI sequences, is 97% to 98%. Our study illustrates the importance of rigorous morphological and morphometric characterization and multi-locus sequencing for the description of new species within the genus Heterorhabditis, serves to clarify the phylogenetic relationships of this important group of biological control agents, and can inform future species descriptions to advance our efforts towards developing more tools for sustainable and environmentally friendly agriculture.

A molecular-based identification resource for the arthropods of Finland

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.

Seeing through sedimented waters: environmental DNA reduces the phantom diversity of sharks and rays in turbid marine habitats

BACKGROUND

Sharks and rays are some of the most threatened marine taxa due to the high levels of bycatch and significant demand for meat and fin-related products in many Asian communities. At least 25% of shark and ray species are considered to be threatened with extinction. In particular, the density of reef sharks in the Pacific has declined to 3-10% of pre-human levels. Elasmobranchs are thought to be sparse in highly urbanised and turbid environments. Low visibility coupled with the highly elusive behaviour of sharks and rays pose a challenge to diversity estimation and biomonitoring efforts as sightings are limited to chance encounters or from carcasses ensnared in nets. Here we utilised an eDNA metabarcoding approach to enhance the precision of elasmobranch diversity estimates in urbanised marine environments.

RESULTS

We applied eDNA metabarcoding on seawater samples to detect elasmobranch species in the hyper-urbanised waters off Singapore. Two genes-vertebrate 12S and elasmobranch COI-were targeted and amplicons subjected to Illumina high-throughput sequencing. With a total of 84 water samples collected from nine localities, we found 47 shark and ray molecular operational taxonomic units, of which 16 had species-level identities. When data were compared against historical collections and contemporary sightings, eDNA detected 14 locally known species as well as two potential new records.

CONCLUSIONS

Local elasmobranch richness uncovered by eDNA is greater than the seven species sighted over the last two decades, thereby reducing phantom diversity. Our findings demonstrate that eDNA metabarcoding is effective in detecting shark and ray species despite the challenges posed by the physical environment, granting a more consistent approach to monitor these highly elusive and threatened species.

A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science

Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called "dark taxon impediment") whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens ("superficial description impediment"). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on COI barcode clusters ("BINs") computed by BOLD Systems. More than 99% of the BINs (387 of 390) were converted into species by assigning binominal names (e.g. BIN "BOLD:ACM9419" becomes Bracon federicomatarritai) and adding a minimal diagnosis (consisting only of a consensus barcode for most species). We here show that many of Sharkey et al.'s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next "superficial description impediment" for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.'s approach of using consensus barcodes as diagnoses is not functional because it cannot be applied consistently. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species, and voice concerns over Sharkey et al.'s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya

BACKGROUND

There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans.

METHODS

Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3-V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database.

RESULTS

cytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by Anaplasma (8.0%), Methylobacterium (3.5%), Delftia (3.8%), Coxiella (2.6%), Bradyrhizobium (1.6%) and Acinetobacter (1.1%). Other less abundant (<1%) and potentially pathogenic included Ehrlichia, Rickettsia, Leptospira, Borrelia, Brucella, Chlamydia and Streptococcus. By Shannon diversity index, Acomys spleens carried more diverse bacteria (mean Shannon diversity index of 2.86, p = 0.008) compared to 1.77 for Crocidura, 1.44 for Rattus, 1.40 for Arvicathis and 0.60 for Mastomys.

CONCLUSION

This study examined systemic bacteria that are filtered by the spleen and the findings underscore the utility of 16S rRNA deep sequencing in characterizing complex microbiota that are potentially relevant to one health issues. An inherent problem with the V3-V4 region of 16S rRNA is the inability to classify bacteria reliably beyond the genera. Future studies should utilize the newer long read methods of 16S rRNA analysis that can delimit the species composition.

Liolophura species discrimination with geographical distribution patterns and their divergence and expansion history on the northwestern Pacific coast

The chiton Liolophura japonica (Lischke 1873) is distributed in intertidal areas of the northwestern Pacific. Using COI and 16S rRNA, we found three genetic lineages, suggesting separation into three different species. Population genetic analyses, the two distinct COI barcoding gaps albeit one barcoding gap in the 16S rRNA, and phylogenetic relationships with a congeneric species supported this finding. We described L. koreana, sp. nov. over ca. 33°24′ N (JJ), and L. sinensis, sp. nov. around ca. 27°02′–28°00′ N (ZJ). We confirmed that these can be morphologically distinguished by lateral and dorsal black spots on the tegmentum and the shape of spicules on the perinotum. We also discuss species divergence during the Plio-Pleistocene, demographic expansions following the last interglacial age in the Pleistocene, and augmentation of COI haplotype diversity during the Pleistocene. Our study sheds light on the potential for COI in examining marine invertebrate species discrimination and distribution in the northwestern Pacific.

A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes

The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based identification and morphological identification of both large (>0.5 mm in length) and small (<0.5 mm in length) invertebrate specimens intercepted at the Australian border. DNA barcode sequencing results supported the morphological identification in most cases and enabled immature stages of invertebrates and their eggs to be identified more confidently. Results also showed that sequencing the COI barcode region using the ONT rapid sequencing principle is a cost-effective and field-adaptable approach for the rapid and accurate identification of invertebrate pests. Overall, the results suggest that MinION sequencing of DNA barcodes offers a complementary tool to the existing morphological diagnostic approaches and provides rapid, accurate, reliable and defendable evidence for identifying invertebrate pests at the border.

Sarcocystis neurona and related Sarcocystis spp. shed by opossums (Didelphis spp.) in South America

Protozoan parasites of the genus Sarcocystis are obligatory heteroxenous cyst-forming coccidia that infect a wide variety of animals and encompass approximately 200 described species. At least four Sarcocystis spp. (S. falcatula, S. neurona, S. lindsayi and S. speeri) use opossums (Didelphis spp.) as definitive hosts, and two of them, S. neurona and S. falcatula, are known to cause disease in horses and birds, respectively. Opossums are restricted to the Americas, but their distribution in the Americas is heterogeneous. Five Didelphis spp. are distributed in South America (D. aurita, D. albiventris, D. marsupialis, D. imperfecta and D. pernigra) whereas just one opossum species (D. virginiana) is found in North America. Studies conducted in the last decades show that Sarcocystis spp., derived from South American Didelphis spp., have biological and genetic differences in relation to Sarcocystis spp. shed by the North American opossum D. virginiana. The aim of this review was to address the peculiar scenario of Sarcocystis species shed by South American opossums, with a special focus on diagnosis, epidemiology, and animal infections, as well as the genetic characteristics of these parasites.