Taxa Research Articles

Evolutionary history shapes variation of wood density of tree species across the world

The effect of evolutionary history on wood density variation may play an important role in shaping variation in wood density, but this has largely not been tested. Using a comprehensive global dataset including 27,297 measurements of wood density from 2621 tree species worldwide, we test the hypothesis that the legacy of evolutionary history plays an important role in driving the variation of wood density among tree species. We assessed phylogenetic signal in different taxonomic (e.g., angiosperms and gymnosperms) and ecological (e.g., tropical, temperate, and boreal) groups of tree species, explored the biogeographical and phylogenetic patterns of wood density, and quantified the relative importance of current environmental factors (e.g., climatic and soil variables) and evolutionary history (i.e., phylogenetic relatedness among species and lineages) in driving global wood density variation. We found that wood density displayed a significant phylogenetic signal. Wood density differed among different biomes and climatic zones, with higher mean values of wood density in relatively drier regions (highest in subtropical desert). Our study revealed that at a global scale, for angiosperms and gymnosperms combined, phylogeny and species (representing the variance explained by taxonomy and not direct explained by long-term evolution process) explained 84.3% and 7.7% of total wood density variation, respectively, whereas current environment explained 2.7% of total wood density variation when phylogeny and species were taken into account. When angiosperms and gymnosperms were considered separately, the three proportions of explained variation are, respectively, 84.2%, 7.5% and 6.7% for angiosperms, and 45.7%, 21.3% and 18.6% for gymnosperms. Our study shows that evolutionary history outpaced current environmental factors in shaping global variation in wood density.

Taphonomy of the middle Miocene regular echinoid spines from Cairo-Suez District, Egypt: Palaeoecological and palaeoenvironmental interpretations

The palaeoecology and palaeoenvironment of a dense cluster of regular echinoid spines that occur in an oyster-rich limestone layer are interpreted based on detailed taphonomic study. The paucispecific macrobenthic assemblage associated with these echinoid spines have been studied in the middle Miocene Geniefa Formation, Gebel Gharra, Cairo-Suez District of Egypt. Both echinoid spines and macrobenthic assemblages are dominated by moderately to well-preserved, moderately packed, highly disarticulated, moderately to poorly sorted, re-oriented, and moderately to highly fragmented specimens, confirming parautochthonous nature of this assemblage. The spines are commonly encrusted and bored. At least four taxonomic groups of encrusters are identified, including juvenile oysters, sheet-like cheilostome bryozoans, serpulids, and balanoid barnacles. The diversity of bioerosional ichnotaxa is moderate and includes Gastrochaenolites, Entobia, Maeandropolydora, Trypanites, and Spirolites. Moreover, some echinoid spines display distinct biting traces of fish, representing the first recorded of fish tooth bite marks on remains of regular echinoid spines from the Miocene deposits of Egypt. The faunal composition and trophic structure of the studied faunal assemblage indicate fully oxygenated and euhaline shallow-marine environment with meso- to eutrophic productivity level. The controlling environmental parameters include substrate consistency, bathymetry, water energy, surface-water productivity, and rate of sedimentation. Furthermore, two scenarios for sclerobionts colonisation and development of fish bite marks have been proposed. In the first syn vivo scenario, predatory fish either focused on the encrusting organisms attached to the spines or attacked the echinoid as a food source, resulting in the separation of spines from their original test during the echinoid’s life. In the second post-mortem scenario, disarticulated spines serve as a hard substrate for the colonisation of sclerobionts. Once again, the spines became subject to attacks by fish that fed on the encrusters, resulting in additional bite marks.

A Revision of the Phylogeny of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as Inferred from Ribosomal and Mitochondrial DNA.

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

Navigating the unknown: assessing anthropogenic threats to beaked whales, family Ziphiidae.

This review comprehensively evaluates the impacts of anthropogenic threats on beaked whales (Ziphiidae)-a taxonomic group characterized by cryptic biology, deep dives and remote offshore habitat, which have challenged direct scientific observation. By synthesizing information published in peer-reviewed studies and grey literature, we identified available evidence of impacts across 14 threats for each Ziphiidae species. Threats were assessed based on their pathways of effects on individuals, revealing many gaps in scientific understanding of the risks faced by beaked whales. By applying a comprehensive taxon-level analysis, we found evidence that all beaked whale species are affected by multiple stressors, with climate change, entanglement and plastic pollution being the most common threats documented across beaked whale species. Threats assessed as having a serious impact on individuals included whaling, military sonar, entanglement, depredation, vessel strikes, plastics and oil spills. This review emphasizes the urgent need for targeted research to address a range of uncertainties, including cumulative and population-level impacts. Understanding the evidence and pathways of the effects of stressors on individuals can support future assessments, guide practical mitigation strategies and advance current understanding of anthropogenic impacts on rare and elusive marine species.

Spatio-temporal variations in the mesozooplankton assemblages off Clarence Island, Magellan Strait, Chile

The seasonality in the light regime from subpolar regions impinges on limitations in the zooplankton dynamics. However, knowledge about seasonal variations in the mesozooplankton assemblages is limited in the southern tip of South America and around the Magellan Strait. Here, we studied the seasonal variation (summer vs. winter) and the spatial distribution (dozens of kilometers) of the mesozooplankton on the occidental shore of Clarence Island, Magellan Strait, Chilean Patagonia. A total of 69 taxonomic groups were identified in the samples, varying from 65 in summer (early March 2020) to 50 in winter (June 2020). Copepods numerically dominated the plankton, particularly Drepanopus forcipatus and Clausocalanus brevipes, although chaetognaths were also abundant in winter. The similarity in the composition was higher for samples collected in summer, whereas in winter there was larger variability in the zooplankton structure. At spatial scale, a large sound at the eastern coast of the island, Dyneley sound showed different composition of copepods compared to other channels both in summer and winter. Seasonal variation was five times larger than the spatial variation in the similarity of the mesozooplankton composition. Finally, higher richness and lower evenness were detected in austral summer, while the opposite was noticed in winter, with differences in alpha-diversity indices between seasons but not among locations. Understanding the drivers of seasonal variability in the zooplankton composition of this extreme ecosystem is essential for predictions of the impacts of salmon farming and climate change in southern Patagonia.

A full-length 18S ribosomal DNA metabarcoding approach for determining protist community diversity using Nanopore sequencing.

Protist diversity studies are frequently conducted using DNA metabarcoding methods. Currently, most studies have utilized short read sequences to assess protist diversity. One limitation of using short read sequences is the low resolution of the markers. For better taxonomic resolution longer sequences of the 18S rDNA are required because the full-length has both conserved and hypervariable regions. In this study, a new primer pair combination was used to amplify the full-length 18S rDNA and its efficacy was validated with a test community and then validated with field samples. Full-length sequences obtained with the Nanopore MinION for protist diversity from field samples were compared with Illumina MiSeq V4 and V8-V9 short reads. Sequences generated from the high-throughput sequencers are Amplicon Sequence Variants (ASVs). Metabarcoding results show high congruency among the long reads and short reads in taxonomic annotation at the major taxonomic group level; however, not all taxa could be successfully detected from sequences. Based on the criteria of ≥95% similarity and ≥1000 bp query length, 298 genera were identified by all markers in the field samples, 250 (84%) were detected by 18S, while only 226 (76%) by V4 and 213 (71%) by V8-V9. Of the total 85 dinoflagellate genera observed, 19 genera were not defined by 18S dinoflagellate ASVs compared to only three among the total 52 diatom genera. The discrepancy in this resolution is due to the lack of taxonomically available 18S reference sequences in particular for dinoflagellates. Overall, this preliminary investigation demonstrates that application of the full-length 18S rDNA approach can be successful in field studies.

Analysing the effects of distance, taxon and biomass on vertebrate detections using bulk-collected carrion fly iDNA.

Invertebrate-derived DNA (iDNA) metabarcoding from carrion flies is a powerful, non-invasive tool that has value for assessing vertebrate diversity. However, unknowns exist around the factors that influence vertebrate detections, such as spatial limits to iDNA signals or if detections are influenced by taxonomic class or estimated biomass of the vertebrates of interest. Using a bulk-collection method, we captured flies from within a zoo and along transects extending 4 km away from this location. From 920 flies, we detected 28 vertebrate species. Of the 28 detected species, we identified 9 species kept at the zoo, 8 mammals and 1 bird, but no reptiles. iDNA detections were highly geographically localized, and only a few zoo animals were detected outside the zoo setting. However, due to the low number of detections in our dataset, we found no influence of the taxonomic group or the estimated biomass of animals on their detectability. Our data suggest that iDNA detections from bulk-collected carrion flies, at least in urban settings in Australia, are predominantly determined by geographic proximity to the sampling location. This study presents an important step in understanding how iDNA techniques can be used in biodiversity monitoring.

Twelve-Year Dynamics of Leading Pathogens Spectrum Causing Orthopedic Infection: A Retrospective Study

Background. The number of surgeries on the musculoskeletal system is increasing every year. Along with the increasing access to orthopedic care, the number of patients with orthopedic infection, the etiological agents of which can be from various taxonomic groups, is also increasing. Staphylococcus aureus and different types of coagulase-negative staphylococci (CoNS), including S. epidermidis and S. lugdunensis, together are the causative agents in 70% of cases.
 Aim of the study — to analyze the dynamics of the microbial spectrum isolated from patients of the septic surgery department for the period from 2011 to 2022.
 Methods. We performed a retrospective analysis of the microbial spectrum isolated from patients who were treated in the septic surgery department from January 1, 2011 to December 31, 2022. The leading pathogens were microorganisms whose share in the spectrum exceeded 3.5%. Of the isolated pathogens, 48.8% were the only etiological agents, and microbial associations were detected in 51.2% of the isolated pathogens.
 Results. A total of 10,327 bacteria strains were identified over the 12-year period. The leading microorganisms causing orthopedic infection were Staphylococcus spp., Enterococcus spp., Propionibacterium spp., Pseudomonas aeruginosa, Corynebacterium spp., Streptococcus spp., Klebsiella spp. and Acinetobacter spp. In the dynamics of isolated pathogens during the analyzed period, several trends were determined: a decrease in the shares of S. aureus, Enterococcus spp., P. aeruginosa, Acinetobacter spp. and an increase in the shares of CoNS and Corynebacterium spp.
 Conclusion. During 12 years, in the microbial spectrum of orthopedic infection in patients of the septic surgery department of our Center, Gram-positive bacteria, in the majority representatives of the genus Staphylococcus, prevailed. At the same time, a significant decrease in the share of S. aureus strains and an increase in the frequency of isolation of various species of CoNS were registered. A significant decrease in the number of non-fermenting Gram-negative bacteria was also revealed.

A preliminary systematic review of the impact of cats on wildlife in the Neotropics

Cats are an invasive alien species that can negatively affect wildlife. However, information regarding their impact on Neotropical wildlife is scattered and limited. We conducted a systematic review to identify studies specifically exploring the impact of cats on wildlife in the Neotropics. In particular, we aimed: 1) to identify the temporal evolution of studies on the impact of cats, as well as bias and gaps that have occurred as a result of their spatial distribution (per country) and the typology of their impact; 2) to identify the Neotropical wildlife species directly affected by cat predation and to categorize these according to their taxonomic groups; 3) to describe the research techniques employed; and 4) to compare the environments evaluated (urban, rural, natural, mixed), as well as the different categories of cats (feral, stray, owned, mixed) involved. We found a total of 55 studies conducted in seven Neotropical countries, with Brazil presenting the most research, but found no research at all in 26 countries. Evaluation of pathogens in cats was the main topic addressed. In total, 215 taxa were reported to be affected by cat predation, with birds being the most frequent. Nine techniques were used in these studies, with blood analysis presented as the most commonly used methodology. Owned cats in urban environments were the most frequently evaluated, and stray cats in mixed environment were the least frequently evaluated. Our results show that cats have a significant negative effect on Neotropical wildlife, and increased studies are therefore a priority.

Salvage Logging and Secondary Succession Promote Spider Diversity in Post-disturbance Stands in Western Germany

Abstract Climate change and biodiversity loss strongly affect ecosystems. In recent years, forests have suffered substantially from climate-induced disturbances resulting in bark beetle outbreaks in coniferous forests. In forest plantations, such disturbances often cause large-scale diebacks, which are frequently salvage-logged. However, the consequences of natural disturbances and subsequent management for forest biodiversity and ecosystem services within plantations are largely unclear. Because they comprise good bioindicators for forest alterations, we here investigated epigeal spider diversity and community composition of three post-disturbance management approaches in former spruce plantations in western Germany. Taxonomic diversity of spiders was significantly enhanced on salvage-logged and secondary succession compared with standing deadwood sites. Nevertheless, the latter provided a refuge for forest specialists, moisture and shade-loving as well as smaller species, whereas the other two management categories were mostly inhabited by larger spiders associated with open habitats. Because all three post-disturbance management approaches harbored highly distinct spider communities and divergent functional guilds, we propose the application of a variety of management approaches for bark beetle-affected spruce plantations. The resulting habitat heterogeneity will likely enhance the biodiversity of spiders and other taxonomic groups. Study Implications: Bark beetle outbreaks became severe disturbances in spruce plantations. The management of affected stands usually aims at mitigating economic losses, but within the current biodiversity crisis, it is increasingly important to consider ecological consequences. This study shows that salvage logging or secondary succession can increase spider taxonomic diversity, although forest species preferred standing deadwood sites. All management categories harbored highly distinct spider assemblages characterized by different ecological and functional guilds. Our results indicated that spider communities were influenced by canopy openness, microclimate, and competition rather than post-disturbance management. Therefore, management practices should include diverse approaches to foster many different spider assemblages.

Bird‐mediated endozoochory as a potential dispersal mechanism of bony fishes

The dispersal of fish into distant and isolated habitats remains a topic of continuous discussion in the field of fish biogeography. This is particularly relevant due to the perceived limitation of fish movement to what is known as active dispersal. Fish migration is often confined to interconnected water bodies, underscoring the significance of dispersal for fish inhabiting isolated aquatic habitats. However, empirical evidence for a natural (i.e. not human‐mediated) mechanism has been limited. Here we explore and provide evidence for waterbird‐mediated endozoochory as a possible dispersal mechanism in various fish species and families. We force‐fed mallards Anas plathyrynchos with fertilised eggs of nine bony fish species, covering nine taxonomic families. We recovered viable embryos of five fish taxa in the faeces of mallard, proving the ability of fish eggs to survive the passing of the digestive system of waterbirds. Moreover, the recovered eggs successfully hatched into larvae in two fish species. Taking into the flight speed and numerosity of mallards, as well as the high abundance of fish eggs, our results highlight endozoochory of fish eggs by waterbirds as a possible significant, although likely rare natural dispersal mechanism that can occur across more species than previously known in freshwater fish.

Effects of management, habitat and landscape characteristics on biodiversity of orchard meadows in Central Europe: A brief review

Increasing agricultural intensification, combined with land transformation and fragmentation, poses significant threats to biodiversity. While extensively cultivated landscapes serve as vital refuges against biodiversity loss, they are modified by land abandonment and intensification. Orchard meadows in Central Europe represent traditional extensive land management systems, exhibiting high biodiversity. Comprising cultivated grasslands and scattered fruit trees, orchard meadows feature structures rich in different habitats supporting a diverse flora and fauna. However, their decreasing economic importance in recent decades has resulted in severe degradation or abandonment. Despite their importance for biodiversity conservation, there remains no comprehensive overview of orchard meadow biodiversity and management in Central Europe. This review aims to summarize existing knowledge on orchard meadows’ role in biodiversity conservation and the effects of management practices on habitat diversity and quality at both smaller (structure and microhabitats, local scale) and larger scales (surrounding landscape, regional scale). The first part focuses on orchard meadow biodiversity, including both plants and animals and their link to landscape-scale factors. Biodiversity in orchard meadows is predominantly affected by patch size, determining species richness and composition, and connectivity to neighbouring orchard meadows, influencing species migration and recolonization success. The second part evaluates management impacts, illustrating differences in the benefits of mowing versus grazing across taxonomic groups. An intermediate management intensity for orchard meadows determines their conservation value in terms of species composition, varying among different taxonomic groups. To prevent area loss and abandonment of orchard meadows, we advocate for political and public support, along with incentives for farmers to maintain their biodiversity.

Scale morphology is a promising, additional tool for exploring the taxonomy and ecology of freshwater fishes

AbstractIt has long been recognized that presence–absence, localisation, size, number and shape of fish scales can be important taxonomic features. Although there are some notes on the relationship between scale morphology and ecological needs, in the absence of a sufficiently large and detailed database, the morphological variability of fish scales and the factors responsible for this variability have not yet been explored in detail. For this reason, a database—which contains the shape and relative size data of 193 freshwater fish taxa of 14 orders, originated from five biogeographic realms—has been built. Database analyses showed that both the scale shape and relative size are proper taxonomic indicators. They can be used to separate higher taxonomic categories (e.g., orders), and by the simultaneous analysis of shape and size scale morphology, we showed increased sensitivity for species‐level detachments. Our results suggest that while both the shape and the size of the fish scales are genetically determined, they are also useful descriptors of the niche segregation (habitat use, flow preference) of close relative species. Scale morphology is a promising additional tool to specify the environmental preferences of lesser known or close relative recent and extinct fish species. And also can be of great help in such cases when only the scales are available for taxonomic identification, for example, in the research field of archaeology and palaeontology.

Response of the symbiotic microbial community of Dioscorea opposita Thunb. cv. Tiegun to root-knot nematode infection.

Yam is an important medicinal and edible dual-purpose plant with high economic value. However, nematode damage severely affects its yield and quality. One of the major effects of nematode infestations is the secondary infection of pathogenic bacteria or fungi through entry wounds made by the nematodes. Understanding the response of the symbiotic microbial community of yam plants to nematodes is crucial for controlling such a disease. In this study, we investigated the rhizosphere and endophytic microbiomes shift after nematode infection during the tuber expansion stage in the Dioscorea opposita Thunb. cv. Tiegun yam. Our results revealed that soil depth affected the abundance of nematodes, and the relative number of Meloidogyne incognita was higher in the diseased soil at a depth of 16-40 cm than those at a depth of 0-15 cm and 41-70 cm. The abundance of and interactions among soil microbiota members were significantly correlated with root-knot nematode (RKN) parasitism at various soil depths. However, the comparison of the microbial alpha diversity and composition between healthy and diseased rhizosphere soil showed no difference. Compared with healthy soils, the co-occurrence networks of M. incognita-infested soils included a higher ratio of positive correlations linked to plant health. In addition, we detected a higher abundance of certain taxonomic groups belonging to Chitinophagaceae and Xanthobacteraceae in the rhizosphere of RKN-infested plants. The nematodes, besides causing direct damage to plants, also possess the ability to act synergistically with other pathogens, especially Ramicandelaber and Fusarium, leading to the development of disease complexes. In contrast to soil samples, RKN parasitism specifically had a significant effect on the composition and assembly of the root endophytic microbiota. The RKN colonization impacted a wide variety of endophytic microbiomes, including Pseudomonas, Sphingomonas, Rhizobium, Neocosmospora, and Fusarium. This study revealed the relationship between RKN disease and changes in the rhizosphere and endophytic microbial community, which may provide novel insights that help improve biological management of yam RKNs.

Persistent homology reveals strong phylogenetic signal in 3D protein structures.

Changes that occur in proteins over time provide a phylogenetic signal that can be used to decipher their evolutionary history and the relationships between organisms. Sequence comparison is the most common way to access this phylogenetic signal, while those based on 3D structure comparisons are still in their infancy. In this study, we propose an effective approach based on Persistent Homology Theory (PH) to extract the phylogenetic information contained in protein structures. PH provides efficient and robust algorithms for extracting and comparing geometric features from noisy datasets at different spatial resolutions. PH has a growing number of applications in the life sciences, including the study of proteins (e.g. classification, folding). However, it has never been used to study the phylogenetic signal they may contain. Here, using 518 protein families, representing 22,940 protein sequences and structures, from 10 major taxonomic groups, we show that distances calculated with PH from protein structures correlate strongly with phylogenetic distances calculated from protein sequences, at both small and large evolutionary scales. We test several methods for calculating PH distances and propose some refinements to improve their relevance for addressing evolutionary questions. This work opens up new perspectives in evolutionary biology by proposing an efficient way to access the phylogenetic signal contained in protein structures, as well as future developments of topological analysis in the life sciences.

Flying by the river side: Survey of bat distributions and environmental contexts along a 1000‐mile river corridor, Green and Colorado Rivers, USA

AbstractAimEmerging research shows how bioindicators, specifically bats, can serve as a means for monitoring conservation and management of riparian corridors for multiple taxonomic groups. To track changes in the composition or abundance of bioindicator species, researchers must attain a baseline in species presence and relative activity. We examined the spatial and temporal patterns of bat community composition and activity along a 1000‐mile river corridor to determine species diversity trends by latitude and habitat.LocationColorado River Basin.MethodsHere we describe the results from an acoustic bat survey conducted opportunistically on the 2019 Sesquicentennial Colorado River Exploring Expedition. This broad, 1000‐mile survey provides a baseline for species distributions over a large geographic range.ResultsIn total, we collected 63 nights of acoustic data over 70 days and recorded over 59,000 files equating to 45,363 caLL files (≥2 pulses). 18,490 (41% of caLL files) were identified as species (n = 19 bat species). We applied non‐metric multidimensional scaling to characterize spatiotemporal patterns of activity between species, as well as compared bat activity among river features and local environmental conditions (i.e., temperature and time since sunset) using an information theoretic approach.ConclusionSpecies composition varied by physiographic region and adjacent river habitat, thus providing a quantifiable measure of determining habitat quality along this major river system and providing baseline information for using bats as bioindicators of habitat quality.

Soil fauna diversity is enhanced by vegetation complexity and no-till planting in regenerative agroecosystems

Agricultural ecosystems are driven by the need to increase yield, due to increased food demands. Conventional, intensive practices are not sustainable as they disrupt the biodiversity in the soil which performs a range of ecosystem functions that sustain soil productivity and resilience. Conservation agriculture and crop-livestock integrated agriculture have been promoted as some of the most sustainable and biodiversity-conserving forms of agriculture. This study assesses how soil macro-and mesofauna in staple crops respond to different agricultural land uses, including conventional, integrated and conservation agriculture, and lastly, natural grassland ecosystems which were used as reference sites. We compared species richness, composition, and functional structure of soil fauna among the land uses and assessed environmental drivers of these patterns. Soil macro-and mesofauna species richness was generally lower in conventional management compared to other management practices, for overall arthropods and for the separate taxonomic groups, beetles, earthworms, spiders, and springtails. Different functional guilds varied in their responses to the farming systems. Vegetation cover and plant litter cover are the variables which benefited most fauna diversity. The practices of no-till plantings coupled with diversified crop rotations and cover crop mixtures under conservation and integrated agricultural management enhances the diversity of earthworms, collembola, beetles, and spiders. Low-disturbance soil management, crop diversification and within-crop habitat complexity preserves arthropod soil fauna diversity in staple crops.

Distribution and Abundance of Zooplankton in Anthropogenic-Impacted Stream, Nsit-Ibom, Nigeria

This study aimed to investigate the distribution and abundance of zooplankton in Mbiokporo stream Nsit-Ibom Local Government Area, Akwa Ibom State, Nigeria. Samples were collected and analyzed using standard methods. The result revealed that there were 9 zooplankton taxonomic groups (namely: Arachnida, Bdelloidae, Branchiopoda, Chromadorae, Euglenoidea, Hexanauplia, Insecta, Polychaeta, Tubulinea), comprising 12 species and 91 individuals. The most abundant zooplankton species was Temora longicornis with the highest number of species across all the stations 24 > 19 > 7 for station 1, station 2, and station 3 respectively. Branchiopoda had the highest number of species (4) and highest species composition (33.33%), while Hexanauplia recorded the highest individual abundance (54.95%). The relative abundance of zooplankton phyla was as follows: (Hexanauplia, 54.95 %) > (Branchiopoda, 13.19 %) > (Bdelloidae, 8.79) % > (Chromadorae, 7.69 %) > (Polychaeta and Arachnida, 5.49 % each) > (Insecta, 2.20 %) > (Tubulinea, 1.10 %) respectively. Indices of species dominance were as follows: station 1 > station 2 > station 3, with the following values 0.4349 > 0.4235 > 0.2397 each. Meanwhile, the highest species evenness was in station 3 (0.7887), followed by station 2 (0.5495), while the lowest was in station 1 (0.486). Margalef’s species diversity was slightly higher in station 1 (1.649) than in station 3 (1.618) while the lowest was in station 2 (1.456). The equitability index among stations was as follows: 3 (0.8675) > station 2 (0.6659) > station 1 (0.6292). However, this result revealed that ongoing anthropogenic activities along the stream may resulted in the deterioration of the stream thereby leading low species composition of zooplankton as observed in this study.

EDNA metabarcoding reveals biodiversity and depth stratification patterns of dinoflagellate assemblages within the epipelagic zone of the western Coral Sea

BackgroundDinoflagellates play critical roles in the functioning of marine ecosystems but also may pose a hazard to human and ecosystem health by causing harmful algal blooms (HABs). The Coral Sea is a biodiversity hotspot, but its dinoflagellate assemblages in pelagic waters have not been studied by modern sequencing methods. We used metabarcoding of the 18 S rRNA V4 amplicon to assess the diversity and structure of dinoflagellate assemblages throughout the water column to a depth of 150 m at three stations in the Western Coral Sea. Additionally, at one station we compared metabarcoding with morphological methods to optimise identification and detection of dinoflagellates.ResultsStratification of dinoflagellate assemblages was evident in depth-specific relative abundances of taxonomic groups; the greatest difference was between the 5–30 m assemblages and the 130–150 m assemblages. The relative abundance of Dinophyceae (photosynthetic and heterotrophic) decreased with increasing depth, whereas that of Syndiniales (parasitic) increased with increasing depth. The composition of major taxonomic groups was similar among stations. Taxonomic richness and diversity of amplicon sequence variants (ASVs) were similar among depths and stations; however, the abundance of dominant taxa was highest within 0–30 m, and the abundance of rare taxa was highest within 130–150 m, indicating adaptations to specific depth strata. The number of unclassified ASVs at the family and species levels was very high, particularly for Syndinian representatives.ConclusionsDinoflagellate assemblages in open water of the Coral Sea are highly diverse and taxonomically stratified by depth; patterns of relative abundance along the depth gradient reflect environmental factors and ecological processes. Metabarcoding detects more species richness than does traditional microscopical methods of sample analysis, yet the methods are complementary, with morphological analysis revealing additional richness. The large number of unclassified dinoflagellate-ASVs indicates a need for improved taxonomic reference databases and suggests presence of dinoflagellate-crypto and–morphospecies.

Spectral Signatures of Macroalgae on Hawaiian Reefs

In Hawaiʻi, native macroalgae or “limu” are of ecological, cultural, and economic value. Invasive algae threaten native macroalgae and coral, which serve a key role in the reef ecosystem. Spectroscopy can be a valuable tool for species discrimination, while simultaneously providing insight into chemical processes occurring within photosynthetic organisms. The spectral identity and separability of Hawaiian macroalgal taxonomic groups and invasive and native macroalgae are poorly known and thus were the focus of this study. A macroalgal spectroscopic library of 30 species and species complexes found in Hawaiʻi was created. Spectral reflectance signatures were aligned with known absorption bands of taxonomic division-specific photosynthetic pigments. Quadratic discriminant analysis was used to explore if taxonomic groups of algae and native versus invasive algae could be classified spectrally. Algae were correctly classified based on taxonomic divisions 96.5% of the time and by species 83.2% of the time. Invasive versus native algae were correctly classified at a rate of 93% and higher, although the number of invasive algal species tested was limited. Analyses suggest that there is promise for the spectral separability of algae investigated in this study by algal taxonomic divisions and native-invasive status. This study created a spectral library that lays the groundwork for testing the spectral mapping of algae using current airborne and forthcoming spaceborne imaging spectroscopy, which could have significant implications for coastal management.