Exceptional Diversity Research Articles

Multi-objective generalized normal distribution optimization: a novel algorithm for multi-objective problems

This study introduces the Multi-objective Generalized Normal Distribution Optimization (MOGNDO) algorithm, an advancement of the Generalized Normal Distribution Optimization (GNDO) algorithm, now adapted for multi-objective optimization tasks. The GNDO algorithm, previously known for its effectiveness in single-objective optimization, has been enhanced with two key features for multi-objective optimization. The first is the addition of an archival mechanism to store non-dominated Pareto optimal solutions, ensuring a detailed record of the best outcomes. The second enhancement is a new leader selection mechanism, designed to strategically identify and select the best solutions from the archive to guide the optimization process. This enhancement positions MOGNDO as a cutting-edge solution in multi-objective optimization, setting a new benchmark for evaluating its performance against leading algorithms in the field. The algorithm's effectiveness is rigorously tested across 35 varied case studies, encompassing both mathematical and engineering challenges, and benchmarked against prominent algorithms like MOPSO, MOGWO, MOHHO, MSSA, MOALO, MOMVO, and MOAOS. Utilizing metrics such as Generational Distance (GD), Inverted Generational Distance (IGD), and Maximum Spread (MS), the study underscores MOGNDO's ability to produce Pareto fronts of high quality, marked by exceptional precision and diversity. The results affirm MOGNDO's superior performance and versatility, not only in theoretical tests but also in addressing complex real-world engineering problems, showcasing its high convergence and coverage capabilities. The source codes of the MOGNDO algorithm are publicly available at https://nimakhodadadi.com/algorithms-%2B-codes.

Hidden hotspots of amphibian biodiversity in China

Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth. Our study combines 20 y of field surveys with new molecular analyses of 521 described species and also identifies 100 potential cryptic species. We identify 10 hotspots of amphibian diversity in China, each with exceptional species richness and endemism and with exceptional phylogenetic diversity and phylogenetic endemism (based on a new time-calibrated, species-level phylogeny for Chinese amphibians). These 10 hotspots encompass 59.6% of China's described amphibian species, 49.0% of cryptic species, and 55.6% of species endemic to China. Only four of these 10 hotspots correspond to previously recognized biodiversity hotspots. The six new hotspots include the Nanling Mountains and other mountain ranges in South China. Among the 186 species in the six new hotspots, only 9.7% are well covered by protected areas and most (88.2%) are exposed to high human impacts. Five of the six new hotspots are under very high human pressure and are in urgent need of protection. We also find that patterns of richness in cryptic species are significantly related to those in described species but are not identical.

Amphibian conservation status in Brazil: Spatial patterns, threats, and challenges

Extinction risk assessments are valuable conservation tools, especially for sensitive groups like amphibians, which are facing escalating threats from habitat loss and degradation. In this scenario, Brazil stands out as a pivotal player in amphibian conservation due to its exceptional amphibian diversity. Between 2010 and 2014, 973 amphibian species were assessed in Brazil. More recently, from 2017 to 2018, this number increased to 1096. In this study, we (1) compare the extinction risk status of Brazilian amphibians between the 1st and 2nd assessments; (2) evaluate the reasons for changes in status; (3) identify the main threats and research recommendations; and (4) analyze the spatial patterns of threatened species in relation to protected areas and ecoregions in Brazil. Our findings reveal an increase in the number of threatened species from the first to the second assessment. The categories of Least Concern and Critically Endangered experienced the most significant increases, with 169 and 16 more species, respectively, while the count of Data Deficient species dropped by 71. The primary factor contributing to these changes is the availability of new, more precise information, affecting 134 species, or 85.4% of the cases. Threatened species are predominantly clustered within the Atlantic Forest biome, itself the most endangered biome in Brazil, hosting 46 species, or 78% of the total. Notably, one-third of threatened species in Brazil do not inhabit protected areas and thus require immediate conservation attention. While substantial progress has been made in understanding Brazilian amphibians in recent years, an urgent need persists for fundamental research. This research should encompass taxonomy, natural history, and the evaluation of threat impacts, providing a robust foundation for more effective conservation efforts concerning this group.

Compact triple band notched UWB MIMO antenna with integrated GSM

SummaryThis paper introduces an innovative four‐element Ultra‐wideband (UWB) MIMO structure featuring an integrated global system for mobile (GSM) antenna with the ability to achieve dual and triple band‐notch capabilities. The antenna's distinctiveness is achieved through the utilization of four directional meandered line shaping decoupling structures (MLSDS), an orthogonal arrangement, and multi‐slot techniques. The incorporation of orthogonal separation alongside four directional MLSDS significantly reduces the mutual interference between radiating elements. By placing MLSDS on both sides of the substrate, effective coverage of the GSM band is achieved. The development of the MIMO structure unfolds through four distinct phases. The initial stage lacks MLSDS, while the second stage incorporates MLSDS. The third and fourth stages respectively introduce MLSDS with dual and triple notch characteristics. The presence of MLSDS enhances the antenna's impedance bandwidth (IBW). The intended notches are tailored to address interference from bands like Band n41, WLAN, and X‐band. Furthermore, the proposed antenna has undergone simulation, measurement, and comparative analysis with existing models, focusing on diversity performance metrics. The results reveal its exceptional diversity performance, positioning it as a potential choice for creating a portable UWB‐MIMO system.

First documentation on herpetofauna diversity in Gunung Belumut Amenity Forest, Peninsular Malaysia: Implications for conservation in an Environmentally Sensitive Area (ESA).

Malaysia is blessed with lush tropical rainforests that harbour an exceptional diversity of amphibians and reptiles. However, compared to other animal groups, amphibians and reptiles have received limited attention in research, despite their ecological significance. With amphibians and reptile species having been declining rapidly due to anthropogenic activities, there is a pressing need to conserve these species and their habitats. Environmentally Sensitive Areas (ESAs) are designated regions that are beneficial due to their critical role in providing essential ecosystem services and serving as repositories of biodiversity. Nonetheless, the classification of ESAs in Malaysia lacks biological elements and only focuses on physical attributes. To enhance the current ESA classification framework by integrating biological components, there is an urgent need to obtain information on diversity and habitat in Malaysia. Therefore, the objectives of this study were twofold: to determine the diversity of amphibians and reptiles in Gunung Belumut Amenity Forest and to conduct a comparative analysis between the herpetofauna assemblages in Gunung Belumut with other forest reserves in Peninsular Malaysia. The survey was carried out between March and June 2022, with additional sampling conducted in February 2023. The Visual Encounter Survey (VES) and pitfall trap methods were employed to survey the herpetofauna species, focusing on both aquatic and terrestrial habitats within the study area. A total of 210 individuals representing 38 species of herpetofauna were recorded, comprising 18 amphibian and 20 reptile species. Amongst the observed species, Limnonectesblythii was the most frequently encountered amphibian, with 59 individuals observed, while the dominant reptile species was Cyrtodactylusconsobrinus, represented by eight individuals. This pioneering study serves as a vital baseline documentation of the amphibian and reptile assemblages in Gunung Belumut Amenity Forest. It provides valuable information for identifying extant herpetofauna species, including those of potential conservation concern or rarity. These findings contribute to ongoing conservation efforts dedicated to the preservation of herpetofauna within the region. By understanding the diversity and distribution patterns of amphibians and reptiles in Gunung Belumut, effective conservation strategies can be developed to protect these species and their habitats.

Four-bar Geometry is Shared among Ecologically DivergentFish Species.

Understanding the factors that influence morphological evolution is a major goal in biology. One such factor is the ability to acquire and process prey. Prey hardness and evasiveness are important properties that can impact evolution of the jaws. Similar diets and biomechanical systems have repeatedly evolved among fish lineages, providing an opportunity to test for shared patterns of evolution across distantly related organisms. Four-bar linkages are structures often used by animals to transmit force and motion during feeding and that provide an excellent system to understand the impact of diet on morphological and biomechanical evolution. Here, we tested how diet influences the evolutionary dynamics of the oral four-bar linkage system in wrasses (Family: Labridae) and cichlids (Family: Cichlidae). We found that shifts in prey hardness/evasiveness are associated with limited modifications in four-bar geometry across these two distantly related fish lineages. Wrasse and cichlid four-bar systems largely exhibit many-to-one mapping in response to dietary shifts. Across two iconic adaptive radiations of fish, an optimal four-bar geometry has largely been co-opted for different dietary functions during their extensive ecological diversification. Given the exceptional jaw diversity of both lineages, many-to-one mapping of morphology to mechanical properties may be a core feature of fish adaptive radiation.

Mazon Creek fossils brought to you by coal, concretions and collectors

Abstract The late Carboniferous (Middle Pennsylvanian, ∼307 Ma ago) Mazon Creek Lagerstätte found in northern Illinois, USA, is unique for its exceptional biotic diversity as well as the human endeavours, both professional and avocational, that brought vast numbers of fossils and new species to science. In 1997, the Mazon Creek Fossil Beds, exposed along the Mazon River near Benson Road, Morris, IL, became a National Historic Landmark. The fossils are preserved in siderite (iron carbonate, FeCO 3 ) concretions within the lower 3–8 m of the Francis Creek Shale Member of the Carbondale Formation, and often retain outlines of original soft tissues. The Mazon Creek biota includes over 465 animal and 350 plant species representing more than 100 orders, which is attributed to the preservation of organisms from multiple habitats and the large number of specimens collected. That phenomenon was made possible by coal extraction bringing concretions to the surface and highly motivated amateur collectors pursuing them. Some of the formerly mined areas continue to draw collectors and are preserved as part of the Mazonia-Braidwood State Fish and Wildlife Area. The fossils, fossil collectors and collection sites are a significant part of the cultural and scientific geoheritage.

Functional iridoid synthases from iridoid producing and non-producing Nepeta species (subfam. Nepetoidae, fam. Lamiaceae).

Iridoids, a class of atypical monoterpenes, exhibit exceptional diversity within the Nepeta genus (subfam. Nepetoidae, fam. Lamiaceae).The majority of these plants produce iridoids of the unique stereochemistry, with nepetalactones (NLs) predominating; however, a few Nepeta species lack these compounds. By comparatively analyzing metabolomics, transcriptomics, gene co-expression, and phylogenetic data of the iridoid-producing N. rtanjensis Diklić & Milojević and iridoid-lacking N. nervosa Royle & Bentham, we presumed that one of the factors responsible for the absence of these compounds in N. nervosa is iridoid synthase (ISY). Two orthologues of ISY were mined from leaves transcriptome of N. rtanjensis (NrPRISE1 and NrPRISE2), while in N. nervosa only one (NnPRISE) was identified, and it was phylogenetically closer to the representatives of the Family 1 isoforms, designated as P5βRs. Organ-specific and MeJA-elicited profiling of iridoid content and co-expression analysis of IBG candidates, highlighted NrPRISE2 and NnPRISE as promising candidates for ISY orthologues, and their function was confirmed using in vitro assays with recombinant proteins, after heterologous expression of recombinant proteins in E. coli and their His-tag affinity purification. NrPRISE2 demonstrated ISY activity both in vitro and likely in planta, which was supported by the 3D modeling and molecular docking analysis, thus reclassification of NrPRISE2 to NrISY is accordingly recommended. NnPRISE also displays in vitro ISY-like activity, while its role under in vivo conditions was not here unambiguously confirmed. Most probably under in vivo conditions the NnPRISE lacks substrates to act upon, as a result of the loss of function of some of the upstream enzymes of the iridoid pathway. Our ongoing work is conducted towards re-establishing the biosynthesis of iridoids in N. nervosa.

Darwin’s overlooked radiation: genomic evidence points to the early stages of a radiation in the Galápagos prickly pear cactus (Opuntia: Cactaceae)

Abstract In the Galápagos Islands, much attention has been devoted to the radiation of iconic species like Darwin’s finches, yet the Galápagos Islands offer an overlooked but equally remarkable opportunity for investigating plant radiations. Using a combination of genomic and phenotypic data, we present evidence of the early stages of a radiation in prickly pear cactus (Opuntia), a lineage widespread across the archipelago. We show that despite extensive ecophenotypic variation, there is limited genomic differentiation, consistent with the hypothesis that Opuntia is in the early stages of the diversification process. Phylogenomic and population genomic analyses show that notwithstanding low genetic differentiation across islands, there is marked geographical structure that is broadly consistent with the palaeogeography of the Galápagos. Because low genetic differentiation stands in stark contrast to the exceptional eco-phenotypic diversity displayed by cacti, it is plausible that the genetic architecture of phenotypic divergence mismatches our genomic sequencing, that phenotypic plasticity precedes genetic divergence and is the source of adaptive evolution, or that introgression influences local adaptation. Models of population relationships including admixture indicate that gene flow is common, probably facilitated by dispersal via animals known to feed on Opuntia flowers, fruits, and seeds. Because the prickly pear cacti of the Galápagos are a radiation in the making, they provide an exciting opportunity to investigate the interplay between ecological and genomic mechanisms promoting diversification.

Sub-1 nm MoS2 and WS2 with extremely enhanced performance

Great efforts have been taken towards in-plane structural extension of two-dimensional materials. Compared with surface lattices, edge lattices represent non-equilibrium states and remain largely unexplored. Herein, we report the all-physical top-down production of sub-1 nm molybdenum disulfide (MoS2) and tungsten disulfide (WS2) with 100% broken lattice. Bulk MoS2 and WS2 are tailored into subnanometer species with satisfactory yields (7.2 and 4.8 wt%) by sequential combination of dual and triple synergy silica-assisted ball-milling. Such two-stage ball-milling push the top-down limit into single-lattice scale, which is far beyond the manufacturing capacity of any known top-down method. Exceptional solvent diversity and solvability of the sub-1 nm MoS2 and WS2 powder endow solution-processability towards hybrid thin film fabrication. The sub-1 nm intrinsic MoS2 and WS2 demonstrate comprehensively superior performances over those of their bulk, nanosheets, and quantum sheets. Both photoluminescence and nonlinear saturation absorption of sub-1 nm MoS2 and WS2 are extremely enhanced. The non-equilibrium states induced by the entirely exposed and broken, intrinsic lattices in sub-1 nm MoS2 and WS2 could be determinative to their extreme performances. Our work highlights the potential of broken lattice and opens up an avenue towards subnanometer materials.

Gigantic animal cells suggest organellar scaling mechanisms across a 50-fold range in cell volume.

The largest cells are orders of magnitude bigger than the smallest cells. Organelle content scales to maintain cell function, with different organelles increasing in volume, length, or number as cells increase in size. Scaling may also reflect functional demands placed on organelles by increased cell size. Amphibians exhibit exceptional diversity in cell size. Using transmission electron microscopy, we analyzed 3 species whose enterocyte cell volumes range from 228 to 10,593 μm3. We show that nuclear volume increases by an increase in radius while mitochondrial volume increases by an increase in total network length; the endoplasmic reticulum and Golgi apparatus, with their complex shapes, are intermediate. Notably, all 4 organelle types increase in total volume proportional to cell volume, despite variation in functional (i.e., metabolic, transport) demands. This pattern suggests that organellar building blocks are incorporated into more or larger organelles following the same rules across species that vary ~50-fold in cell sizes, consistent with a "limited precursor" model for organellar scaling that, in turn, assumes equivalent cytoplasmic concentrations of organellar building block proteins. Taken together, our results lead us to hypothesize that salamanders have evolved increased biosynthetic capacity to maintain functional protein concentrations despite huge cell volumes.

The role of CE16 exo-deacetylases in hemicellulolytic enzyme mixtures revealed by the biochemical and structural study of the novel TtCE16B esterase

Acetyl esterases belonging to the carbohydrate esterase family 16 (CE16) is a growing group of enzymes, with exceptional diversity regarding substrate specificity and regioselectivity. However, further insight into the CE16 specificity is required for their efficient biotechnological exploitation. In this work, exo-deacetylase TtCE16B from Thermothelomyces thermophila was heterologously expressed and biochemically characterized. The esterase targets positions O-3 and O-4 of singly and doubly acetylated non-reducing-end xylopyranosyl residues, provided the presence of a free vicinal hydroxyl group at position O-4 and O-3, respectively. Crystal structure of TtCE16B, the first representative among the CE16 enzymes, in apo- and product-bound form, allowed the identification of residues forming the catalytic triad and oxyanion hole, as well as the structural elements related to the enzyme preference for oligomers. The role of TtCE16B in hemicellulose degradation was investigated on acetylated xylan from birchwood and pre-treated beechwood biomass. TtCE16B exhibited complementary activity to commercially available OCE6 acetylxylan esterase. Moreover, it showed synergistic effects with SrXyl43 β-xylosidase. Overall, supplementation of xylan-targeting enzymatic mixtures with both TtCE16B and OCE6 esterases led to a 3-fold or 4-fold increase in xylose release, when using TmXyn10 and TtXyn30A xylanases respectively.

Pyrrolizidine Alkaloids-Pros and Cons for Pharmaceutical and Medical Applications.

Heterocyclic organic compounds named pyrrolizidine alkaloids (PAs) belong to a group of alkaloids and are synthesized by either plants or microorganisms. Therefore, they are naturally occurring secondary metabolites. They are found in species applied in the pharmaceutical and food industries, thus a thorough knowledge of their pharmacological properties and toxicology to humans is of great importance for their further safe employment. This review is original because it synthesizes knowledge of plant and microbial PAs, which is unusual in the scientific literature. We have focused on the Boraginaceae family, which is unique due to the exceptional richness and diversity of its PAs in plant species. We have also presented the microbial sources of PAs, both from fungi and bacteria. The structure and metabolism of PAs have been discussed. Our main aim was to summarize the effects of PAs on humans, including both negative, toxic ones, mainly concerning hepatotoxicity and carcinogenicity, as well as potentially positive ones for pharmacological and medical applications. We have collected the results of studies on the anticancer activity of PAs from plant and microbial sources (mainly Streptomyces strains) and on the antimicrobial activity of PAs on different strains of microorganisms (bacteria and fungi). Finally, we have suggested potential applications and future perspectives.

HERPETOFAUNA OF THE “EL MINERAL DE NUESTRA SEÑORA DE LA CANDELARIA” RESERVE: A BIOLOGICAL TREASURE IN SINALOA, MEXICO

Mexico hosts an exceptional diversity of approximately 1 421 species of amphibians and reptiles, many of which are endemic to the country. However, the Sinaloa region has remained largely unexplored due to access challenges and social conflicts. This study focuses on analyzing the biodiversity of amphibians and reptiles in the “El Mineral de Nuestra Señora de la Candelaria” reserve in Sinaloa, Mexico. This reserve, located in the Sierra Madre Occidental, covers 1 256 hectares of diverse habitats, including tropical deciduous and sub-deciduous forests. Through fieldwork conducted between 2017 and 2020, 55 species of amphibians and reptiles were documented in the reserve, of which 34 are endemic to Mexico, highlighting its importance as a refuge for native biodiversity. Furthermore, 20 species are protected by Mexican regulations and are listed on the IUCN Red List, indicating their threatened status. This reserve significantly contributes to Sinaloa’s herpetofaunal landscape, safeguarding approximately 32.4% of its diversity and over 53% of the genera present in the state. The presence of endemic and endangered species underscores the need for specific conservation measures. In conclusion, this listing provides a detailed insight into the biological richness of amphibians and reptiles in the “El Mineral de Nuestra Señora de la Candelaria” reserve, emphasizing its value as a refuge for unique and threatened species. The results urge the implementation of effective conservation strategies to protect these unique ecosystems in the context of global environmental changes.

Atlas of Australasian hormurid scorpions. I. The genus Hormurus Thorell, 1876 in Papua New Guinea. Exceptional morphological diversity in male and female copulatory structures suggests genital coevolution

Atlas of Australasian hormurid scorpions. I. The genus Hormurus Thorell, 1876 in Papua New Guinea. Exceptional morphological diversity in male and female copulatory structures suggests genital coevolution

Virulence Associations and Global Context of AvrStb6 Genetic Diversity in Iranian Populations of Zymoseptoria tritici.

Managing pathogen damage in wheat production is important for sustaining yields. Fungal plant pathogen genomes encode many small secreted proteins acting as effectors that play key roles in the successful colonization of host tissue and triggering host defenses. AvrStb6 is the first described Zymoseptoria tritici avirulence effector, which triggers Stb6-mediated immunity in the wheat host in a gene-for-gene manner. Evasion of major resistance factors such as Stb6 challenges deployment decisions on wheat cultivars. In this study, we analyzed the evolution of the AvrStb6 effector in Iranian isolates of Z. tritici. In total, 78 isolates were isolated and purified from 30 infected wheat specimens collected from the East Azerbaijan and Ardabil provinces of Iran. The pathogenicity of all isolates was evaluated on the susceptible wheat cultivar 'Tajan'. A subset of 40 isolates were also tested for pathogenicity on the resistant cultivar 'Shafir' carrying Stb6. Genetic diversity at the AvrStb6 locus was analyzed for 14 isolates covering the breadth of the observed disease severity. The AvrStb6 sequence variation was high, with virulent isolates carrying highly diverse AvrStb6 haplotypes. In an analysis including more than 1,000 additional AvrStb6 sequences from a global set of isolates, we found that virulent isolates carried AvrStb6 haplotypes either clustering with known virulent haplotypes on different continents or constituting previously unknown haplotypes. Furthermore, we found that AvrStb6 variants from avirulent isolates clustered with known avirulent genotypes from Europe. Our study highlights the relevance of AvrStb6 for Z. tritici virulence and the exceptional global diversity patterns of this effector.

Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences.

The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.

Natural tourist resources in the Stara planina tourist region (Bulgaria)

Abstract The Stara planina tourist region is one of the most attractive regions for tourism in Bulgaria and one of the few that have almost year-round tourist activities. The outline of the area includes the mountain of the same name, but also the Pre-Balkan. This fact predetermines the exceptional richness and diversity of natural tourist resources. Here are some of the largest broad-leaved forests in the country, waterfalls, bizarre rock formations, etc. The relatively well-preserved natural environment is a prerequisite for the presence of exceptional biodiversity, as well as a significant number of protected areas. The region is specialized mainly in mountain tourism, including recreation, mountain trekking, rural and ecotourism. Due to the scarce tourist infrastructure, ski tourism still lags behind in its development compared to other mountain regions in the country. Very often, the Stara planina Region is primarily identified with its cultural and historical heritage, while its natural features remain in the background. Regardless of this, and as a result of the more intense tourist load, the problem of protecting natural tourist resources from the growing anthropogenic pressure is gaining special relevance. There is also an urgent need to identify and evaluate the prospects for sustainable development of the tourism industry in the region. The purpose of the present study is to valorize the natural tourist resources of the Stara planina tourist region and to provide guidelines for their sustainable use.

Spatial transcriptomics in neuroscience.

The brain is one of the most complex living tissue types and is composed of an exceptional diversity of cell types displaying unique functional connectivity. Single-cell RNA sequencing (scRNA-seq) can be used to efficiently map the molecular identities of the various cell types in the brain by providing the transcriptomic profiles of individual cells isolated from the tissue. However, the lack of spatial context in scRNA-seq prevents a comprehensive understanding of how different configurations of cell types give rise to specific functions in individual brain regions and how each distinct cell is connected to form a functional unit. To understand how the various cell types contribute to specific brain functions, it is crucial to correlate the identities of individual cells obtained through scRNA-seq with their spatial information in intact tissue. Spatial transcriptomics (ST) can resolve the complex spatial organization of cell types in the brain and their connectivity. Various ST tools developed during the past decade based on imaging and sequencing technology have permitted the creation of functional atlases of the brain and have pulled the properties of neural circuits into ever-sharper focus. In this review, we present a summary of several ST tools and their applications in neuroscience and discuss the unprecedented insights these tools have made possible.

Early Pliocene otolith assemblages from the outer-shelf environment reveal the establishment of mesopelagic fish fauna over 3 million years ago in southwestern Taiwan

Understanding the diversity of deep-sea fish fauna based on otoliths in the tropical and subtropical West Pacific has been limited, creating a significant knowledge gap regarding regional and temporal variations in deep-sea fish fauna. To address this gap, we collected a total of 122 bulk sediment samples from the Lower Pliocene Gutingkeng Formation in southwestern Taiwan to reconstruct the otolith-based fish fauna. Using planktonic foraminiferal biostratigraphy, we determined the age of the samples to be 5.6 to 3.1 Ma. A total of 8314 otoliths were assigned to 64 different taxa from 33 families, including the discovery of one new genus, Gutingichthys gen. nov., and three new species: Benthosema duanformis sp. nov., Benthosema parafibulatum sp. nov., and Gutingichthys changi sp. nov. Comparisons with other regional otolith-based assemblages highlighted the exceptional diversity of our collection, making it the most diverse fossil fish fauna reported from Taiwan to date. Otolith diversity analysis revealed very few taxa were dominant in the assemblage, particularly the mesopelagic Myctophidae, with a wide variety of minor taxa. The co-occurrence of shallow-water elements suggests episodic storm events as a potential source. The predominance of deep-sea and oceanic fishes indicated an outer-shelf to upper slope environment, resembling the modern outer-shelf and upper slope fish fauna in the region. Our findings suggest an early establishment and persistent presence of the mesopelagic fish community since the Early Pliocene. Further investigations of the Upper Miocene and Pleistocene sections of the Gutingkeng Formation would provide valuable insights into the evolution of deep-sea fish fauna in the area.