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Across Africa, space for conservation is sometimes limited to formally protected areas that have become progressively more isolated. There is a need for targeted conservation initiatives such as the demarcation of landscape connections, defined as areas that encompass environmental variables that promote the natural movement of individuals between populations, which can facilitate gene flow. Landscape connections can mitigate genetic isolation, genetic drift, and inbreeding, which can occur in isolated populations in protected areas. Promoting gene flow can reduce the risk of extirpation often associated with isolated populations. Here we develop and test models for identifying landscape connections among African savannah elephant (Loxodonta africana) populations by combining habitat suitability modeling with gene flow estimates across a large region including seven countries. We find a pronounced non-linear response to unsuitable habitat, consistent with previous studies showing that non-transformed habitat models are poor predictors of gene flow. We generated a landscape connections map that considers both suitable habitats based on telemetry occurrence data and gene flow estimated as the inverse of individual genetic distance, delineating areas that are important for maintaining elephant population connectivity. Our approach represents a novel framework for developing spatially and genetically informed conservation strategies for elephants and many other taxa distributed across heterogeneous and fragmented landscapes. [ABSTRACT FROM AUTHOR]

While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co‐occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 Pocillopora corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of Pocillopora, most of which cannot be reliably identified based on morphology: P. meandrina (42.9%), P. tuahiniensis (25.1%), P. verrucosa (12.2%), P. acuta (10.4%), P. grandis (7.73%), and P. cf. effusa (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used psbAncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of Pocillopora species differed across habitats within the reef. Sister taxa P. verrucosa and P. tuahiniensis had similar niche breadths and hosted the same specialist symbiont species (mostly Cladocopium pacificum) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa P. meandrina and P. grandis had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly C. latusorum). Pocillopora acuta had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, Durusdinium gynnii. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth—Pocillopora species with a broader habitat niche also had a broader symbiont niche. Our results show how fine‐scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated. [ABSTRACT FROM AUTHOR]

There is growing interest in working with beavers (Castor canadensis and Castor fiber) to restore and maintain ecosystem function, improve hydrologic conditions and build climate resiliency in freshwater ecosystems. Beaver translocation into historically occupied but degraded systems has been increasingly applied as a restoration practice over the last two decades. Knowledge of beaver distributions on the landscape is critical to understanding where and when beaver translocations may be effective. However, current understanding of beaver occupancy and translocation success is limited by uncertainty, subjectivity and inefficiency associated with available monitoring methods. We evaluated the efficacy and spatial inference associated with environmental DNA (eDNA) techniques for detecting beaver presence in natural wetland and stream systems in the Cascade mountains of Washington State. We conducted eDNA sampling paired with radio‐tracking of translocated beavers at four relocation sites from October 2020 through October 2022 to elucidate spatial patterns of site use, eDNA detection probability and eDNA quantity. We found that eDNA techniques detected beaver rapidly over long distances – up to 2.9 km from known locations within the first week after release – and reliably detected beavers when they were upstream, with positive detections in 92.4% of downstream eDNA samples collected 1–3 months after release. We also found that eDNA quantity decreased with increasing distance from beaver and increased with the amount of upstream beaver activity. Our study suggests that eDNA is a sensitive tool for monitoring translocated beaver and can provide spatial information on beaver location and site use within a stream system. Hence, eDNA methods could be a valuable tool for rapid inventory and assessment of beaver occupancy and our findings highlight important implications for using eDNA to monitor other semi‐aquatic mammal species that share similar life histories. [ABSTRACT FROM AUTHOR]

Butyrate‐producing bacteria colonise the gut of humans and non‐human animals, where they produce butyrate, a short‐chain fatty acid with known health benefits. Butyrate‐producing bacteria also reside in soils and soil bacteria can drive the assembly of airborne bacterial communities (the aerobiome). Aerobiomes in urban greenspaces are important reservoirs of butyrate‐producing bacteria as they supplement the human microbiome, but soil butyrate producer communities have rarely been examined in detail. Here, we studied soil metagenome taxonomic and functional profiles and soil physicochemical data from two urban greenspace types: sports fields (n = 11) and nature parks (n = 22). We also developed a novel method to quantify soil butyrate and characterised the in situ activity of butyrate‐producing bacteria. We show that soil butyrate was higher in sports fields than nature parks and that sports fields also had significantly higher relative abundances of the terminal butyrate production genes buk and butCoAT than nature parks. Soil butyrate positively correlated with buk gene abundance (but not butCoAT). Soil moisture (r =.50), calcium (r = −.62), iron (ρ =.54), ammonium nitrogen (ρ =.58) and organic carbon (r =.45) had the strongest soil abiotic effects on soil butyrate concentrations and iron (ρ =.56) and calcium (ρ = −.57) had the strongest soil abiotic effects on buk read abundances. Overall, our findings contribute important new insights into the role of sports fields as key exposure reservoirs of butyrate producing bacteria, with important implications for the provision of microbiome‐mediated human health benefits via butyrate. [ABSTRACT FROM AUTHOR]

Context: DNA recovered from predator faeces (scats) can be used to determine the presence of fauna and shed light on their life histories and inter-species interactions. DNA metabarcoding, which involves concurrent amplification and sequencing of DNA from multiple taxa, represents an important advance by enabling the simultaneous detection of multiple species from such samples. Although an attractive proposition, metabarcoding requires 'universally' applicable genetic markers that can discriminate among a broad range of taxa, while also targeting sequences that are sufficiently short to be amplified from degraded DNA. Aims: To identify, evaluate, and test metabarcoding DNA markers suitable for the detection of marsupials and other Australian fauna from terrestrial predator scats found in nature. Methods: We apply a bioinformatic approach using publicly available DNA databases and a locally derived and marker-specific reference-DNA database to evaluate the diagnostic ability and likelihood of amplification of candidate metabarcoding markers for marsupials and other taxa that may be consumed by predators. Key results: We identify two markers (12SV5 and 16SMam) that are suitable for use and successfully identify marsupial sequences at a high level of resolution. These markers work best in combination because they bring complementary levels of primer specificity and diagnostic ability in detecting multiple prey species as well as the predator. We also show that these samples work well in predator scats sampled from the wild in Tasmania. Conclusions: These markers provide a useful tool for surveying mammalian predators and their prey and could also be applied to eDNA analyses from other sample types. Improvements to the reference database and further development of markers targeting different taxonomic groups will improve the resolution and usefulness of this approach. Implications: Metabarcoding of predator scats provides a potent approach to non-invasive wildlife survey that offers the opportunity for the detection of multiple species across all vertebrates. DNA recovered from predator faeces can be used to determine the presence of fauna and shed light on their life histories and inter-species interactions. We identified two markers (12SV5 and 16SMam) that, in combination, are suitable for successfully identifying marsupial sequences at a high level of resolution. We also showed that these samples work well in predator scats sampled from the wild, providing a potent approach to non-invasive wildlife survey, and therefore management, through the detection of multiple species across all vertebrates. Photograph by Anna MacDonald. [ABSTRACT FROM AUTHOR]

Pampas and crab-eating foxes are medium-sized canids living in sympatry in the middle east of South America. Studies on the diet composition of these species provide a deep understanding of their ecological roles in the ecosystem structure and regulation. Using the metabarcoding technique, we analyzed the diet of both fox species in order to identify the vertebrate taxa included as food items. A fragment of the 12S ribosomal gene of the mtDNA was amplified using DNA extracted from 27 scat samples collected in south-central Uruguay during cold (June 2015) and warm (January April 2016) seasons. A fox DNA blocking primer was designed to minimize the host amplicon products, and pooled samples were sequenced through paired-end reads (100 bp library) on a MiSeq Illumina Platform. The generated sequences were compared to a reference database built with sequences available in GenBank. In concordance with previous studies using traditional methods, we found that the most common food taxon were rodents. Qualitative differences in diet composition between both fox species were identified. Armadillo species were only found in pampas fox diet, while a greater variety of amphibians and birds were detected in crab-eating fox feces. Additionally, an innovative approach to differentiate between real and artifact sequences was employed. This method was based on comparing mutations at conserved and non-conserved positions within the secondary structure of the 12S rRNA, combined with network sequence reconstruction. Our results demonstrate the efficacy of the methodology in detecting the food species present in both fox diets, enabling the evaluation of intraspecific diversity among these species and facilitating the discarding of sequencing errors. This makes the methodology applicable to a wide range of studies. [ABSTRACT FROM AUTHOR]

Carassius gibelio (Prussian carp) is the latest invader of Canada's fresh waters, with reports of its presence in Alberta and Saskatchewan. Morphological similarities with introduced C. auratus (goldfish) and the putatively introduced (but likely misidentified) C. carassius (crucian carp) make it difficult to distinguish these species without careful examination. DNA barcoding of the mitochondrial cytochrome c oxidase I (COI) gene is a potential tool to identify Carassius individuals to species, but incorrect annotations of publicly-available sequences can confound attempts at species identification. Here we use morphology and DNA barcoding to identify putative C. gibelio specimens collected from two Alberta locations that constituted new records for the province. Morphologically, specimens were consistent with C. gibelio but were in the range for both C. gibelio and C. auratus. Genetically, our samples could not be identified to species level, being a 100% match with multiple Carassius species. Haplotype networks, however, supported the identification of Alberta carp as C. gibelio, in agreement with statistical analysis. Furthermore, the Alberta haplotype was shared with a fish reported from the seafood trade, suggesting a possible source of entry into Alberta. Therefore, although the BOLD algorithm would suggest the COI gene is not a strong candidate for species-level identification of Carassius species, a haplotype network approach and statistical examination of variability among haplotypes can be used to make reasonable inferences as to species identity. Early detection and management of Carassius species are of critical importance due to their projected ecological impact in Canada; DNA barcoding is one important tool for species identification, especially when specimens are within the phenotypic range expected for multiple species. [ABSTRACT FROM AUTHOR]

Russula griseocarnosa, an edible and medicinal mushroom abundant in nutrients and notable bioactivities, is predominantly grown in the broad-leaved forest with trees of the family Fagaceae in southern China. This species forms ectomycorrhizal associations with plant roots and cannot be artificially cultivated currently. Previous research indicates a strong correlation between the growth of R. griseocarnosa and factors such as the host plant, climate variables (specifically mean temperature and precipitation from June to October), and the rhizosphere microbiota of its habitat. However, comprehensive studies on the fundamental biology of this species are lacking. The interaction between R. griseocarnosa and its host plant, as well as the mechanisms underlying the microbial community dynamics within its habitat, remain ambiguous. The limited repertoire and diversity of carbohydrate-active enzymes (CAZymes) in R. griseocarnosa relative to saprophytic fungi may contribute to its recalcitrance to cultivation on synthetic media. The specific core enzyme and the substances provided by the host plant to facilitate growth are yet to be elucidated, posing a significant challenge in the artificial cultivation of R. griseocarnosa. The habitat of R. griseocarnosa harbours unique microbial communities, indicating the presence of potentially beneficial microorganisms that could be exploited for artificial propagation and conservation efforts. However, the lack of definitive functional verification experiments hinders the realization of this promising prospect. This review offers a comprehensive overview of the nutritional profile and health benefits of R. griseocarnosa, emphasizing recent developments in its isolation, molecular ecology, and artificial cultivation. Additionally, it explores prospective advancements in R. griseocarnosa research, aiming to enrich our foundational understanding for applied purposes and fostering progress in the realm of ectomycorrhizal edible mushrooms. [ABSTRACT FROM AUTHOR]

Biomonitoring of agriculturally important insects is increasingly vital given our need to understand: (a) the severity of impacts by pests and pathogens on crop yield and health and (b) the impact of environmental change and land management on insects, in line with sustainable development and global conservation targets. Traditional entomological traps remain an important part of the biomonitoring toolbox, but sample processing is laborious and introduces latency, and accuracy can be variable. The integration of molecular techniques such as environmental DNA and DNA metabarcoding into insect biomonitoring has gained increasing attention, but the advantages of doing so, the kind of data this can generate, and how easily and effectively molecular analyses can be integrated with the diverse types of entomological traps currently used remains relatively unclear. In this review, we examine how combining DNA metabarcoding with a range of conventional and unconventional entomological sampling techniques can advance biomonitoring in a way that is useful to researchers and practitioners. We highlight some of the key challenges and how to mitigate them, using examples of its integration with different sampling methods from the literature (e.g., interception, pitfall and sticky traps) to demonstrate efficacy and suitability. We discuss how metabarcoding data can be used to infer ecological networks, emphasizing the importance of this as a framework for understanding species interactions and ecosystem functioning for more effective and descriptive biomonitoring. Finally, future advances in biomonitoring are highlighted, alongside recommendations of best practice for researchers both new to and experienced in invertebrate biomonitoring with metabarcoding. [ABSTRACT FROM AUTHOR]

Simple Summary: This study investigates the genetic structure and population dynamics of invasive bullfrogs in China employing cutting-edge genomic technologies. By analyzing microsatellite loci and single nucleotide polymorphisms (SNPs), the study identifies three distinct genetic subpopulations of bullfrogs and explores their origins and dispersal pathways. Findings reveal the varying degrees of gene flow between the subpopulations and a severe bottleneck effect followed by a rapid population expansion. Comparison with American bullfrog populations highlights the differences in genetic diversity and suggests potential multiple introductions. The introduction and subsequent range expansion of the American bullfrog (Lithobates catesbeianus) is part of a rising trend of troublesome biological invasions happening in China. This detrimental amphibious invasive species has strong adaptability. After its introduction and spread, it established its own ecological niche in many provinces of China, and its range has continued to expand to more areas. Previous studies recorded the introduction time of bullfrogs and calculated the changes in their genetic diversity in China using mitochondria, but the specific introduction route in China is still unknown. Expanding upon previous research, we employed whole-genome scans (utilizing 2b-RAD genomic sequencing) to examine single nucleotide polymorphisms (SNPs) and microsatellites within Lithobates catesbeianus to screen the genomes of these invasive amphibian species from eight Chinese provinces and two U.S. states, including Kansas, where bullfrogs originate. A total of 1,336,475 single nucleotide polymorphic loci and 17 microsatellite loci were used to calculate the genetic diversity of bullfrogs and their migration pathways. Our results suggest that the population in Hunan was the first to be introduced and to spread, and there may have been multiple introductions of subpopulations. Additionally, the genetic diversity of both the SNP and microsatellite loci in the Chinese bullfrog population was lower than that of the US population due to bottleneck effects, but the bullfrogs can adapt and spread rapidly. This study will offer crucial insights for preventing and controlling future introductions into the natural habitats in China. Additionally, it will assist in devising more precise strategies to manage the existing populations and curtail their continued expansion, as well as aim to improve clarity and originality while mitigating plagiarism risk. [ABSTRACT FROM AUTHOR]

Mucilage events are among the most conspicuous phenomena in marine ecosystems and present numerous challenges in determining the composition of communities associated with them. To overcome this problem, we used environmental DNA (eDNA) metabarcoding approaches to reveal the species-level resolution of community composition. Mucilaginous aggregates were sampled at six collecting sites during a novel mucilage event (autumn 2021--summer 2022) in the Sea of Marmara, Türkiye. A wide range of plankton community compositions was detected in mucilage samples. eDNA metabarcoding was effective in predicting the community composition of mucilage, which is composed of a wide variety of organisms from mucilaginous aggregates. [ABSTRACT FROM AUTHOR]

Abstract While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co‐occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 Pocillopora corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of Pocillopora, most of which cannot be reliably identified based on morphology: P. meandrina (42.9%), P. tuahiniensis (25.1%), P. verrucosa (12.2%), P. acuta (10.4%), P. grandis (7.73%), and P. cf. effusa (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used psbAncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of Pocillopora species differed across habitats within the reef. Sister taxa P. verrucosa and P. tuahiniensis had similar niche breadths and hosted the same specialist symbiont species (mostly Cladocopium pacificum) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa P. meandrina and P. grandis had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly C. latusorum). Pocillopora acuta had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, Durusdinium gynnii. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth—Pocillopora species with a broader habitat niche also had a broader symbiont niche. Our results show how fine‐scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated.

Abstract Butyrate‐producing bacteria colonise the gut of humans and non‐human animals, where they produce butyrate, a short‐chain fatty acid with known health benefits. Butyrate‐producing bacteria also reside in soils and soil bacteria can drive the assembly of airborne bacterial communities (the aerobiome). Aerobiomes in urban greenspaces are important reservoirs of butyrate‐producing bacteria as they supplement the human microbiome, but soil butyrate producer communities have rarely been examined in detail. Here, we studied soil metagenome taxonomic and functional profiles and soil physicochemical data from two urban greenspace types: sports fields (n = 11) and nature parks (n = 22). We also developed a novel method to quantify soil butyrate and characterised the in situ activity of butyrate‐producing bacteria. We show that soil butyrate was higher in sports fields than nature parks and that sports fields also had significantly higher relative abundances of the terminal butyrate production genes buk and butCoAT than nature parks. Soil butyrate positively correlated with buk gene abundance (but not butCoAT). Soil moisture (r = .50), calcium (r = −.62), iron (ρ = .54), ammonium nitrogen (ρ = .58) and organic carbon (r = .45) had the strongest soil abiotic effects on soil butyrate concentrations and iron (ρ = .56) and calcium (ρ = −.57) had the strongest soil abiotic effects on buk read abundances. Overall, our findings contribute important new insights into the role of sports fields as key exposure reservoirs of butyrate producing bacteria, with important implications for the provision of microbiome‐mediated human health benefits via butyrate.

Blue whales (Balaenoptera musculus) are the largest living animal and, like other baleen whales, became endangered due to whaling. Here, we used population genomics to infer the number, distribution and other characteristics of subspecies and populations. We used the largest DNA dataset in blue whales, both in terms of genomic markers (16,661 SNPs and mtDNA) and geographic coverage (n = 276 for SNPs; n = 531 for mtDNA). We found greatest divergence among the eastern Pacific, Indo‐western Pacific and Antarctic blue whales. There were indications that natural selection in different environments promoted divergence among these groupings. Within these regions, there was divergence between the eastern North and eastern South Pacific, and among the eastern Indian Ocean, the western South Pacific and the northern Indian Ocean. There was no divergence within the Antarctic. These findings are consistent with the current classification of Antarctic and Indo‐western Pacific blue whales in the Southern Hemisphere as different subspecies but call into question the subspecies taxonomy of eastern Pacific blue whales. The study shows that opposite breeding seasons on either side of the equator do not necessarily inhibit connectivity across the equator, and reinforces that population structure needs to be well understood to conserve the diversity within species. [ABSTRACT FROM AUTHOR]

During the present biodiversity crisis, rare and endangered plants can be conserved ex situ in botanic gardens or seed banks. Ex situ collections distributed among multiple locations—"metacollections"—can safeguard against extinction but must represent adequate genetic diversity to be resilient to changing environments. Previous analyses have revealed strategies to create genetically diverse metacollections of plants with diverse life histories. However, past work has neglected important aspects of metacollection conservation: rare alleles, redundancy (duplication of alleles to be resilient to loss), geographic coverage, and relatedness. Therefore, we assessed two existing large metacollections (>250 individuals) of two International Union for Conservation of Nature (IUCN) Red List threatened plant species— Quercus acerifolia , a wind-pollinated oak, and Zamia integrifolia , an insect-pollinated cycad—for these previously neglected aspects of metacollection genetic conservation. We found that large metacollections of both species conserved genetic diversity well: over 80% of all alleles were conserved in at least one copy, and ∼70% of alleles were represented in five to 10 copies. Metacollections, however, could still be improved. The rare genetic diversity of Z. integrifolia was less well conserved than that of Q. acerifolia , and several wild populations of both species are precariously undersampled. Ex situ collections also contained high relatedness, which may hamper restoration efforts. Although large metacollections are commendable for their size and breadth, examining metacollections for these facets allowed a more holistic evaluation of genetic diversity conservation. [ABSTRACT FROM AUTHOR]

Insects are essential not only for ecosystem functioning and food security but also comprise some of the world's most destructive invasive species. Therefore, both insect declines and invasions raise major conservation concerns globally and call for respective conservation or mitigation measures. However, studies of insects are hampered by intrinsic biological features of these organisms, which include extreme population fluctuations, a huge diversity of ecological strategies, and common cryptic species. Population genetics provides a large toolkit to adequately accommodate those features, thereby enabling researchers to inform and monitor the efficacy of conservation and mitigation programs. Here, we provide an overview of the molecular and analytical methods that are relevant to insect conservation or mitigation and highlight the challenges involved in their implementation. We detail how and why temporal changes in genetic diversity, population structure and migration, and the genetic basis of adaptation should be taken into account to inform insect management programs. Finally, we review the barriers to the broad adoption of population genetics in insect research and provide guidelines to facilitate the use of these methods by stakeholders. Overall, this review provides theoretical and practical guidelines for implementing population genetics in both insect conservation and control. [ABSTRACT FROM AUTHOR]

Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here. [ABSTRACT FROM AUTHOR]

Pampas and crab-eating foxes are medium-sized canids living in sympatry in the middle east of South America. Studies on the diet composition of these species provide a deep understanding of their ecological roles in the ecosystem structure and regulation. Using the metabarcoding technique, we analyzed the diet of both fox species in order to identify the vertebrate taxa included as food items. A fragment of the 12S ribosomal gene of the mtDNA was amplified using DNA extracted from 27 scat samples collected in south-central Uruguay during cold (June 2015) and warm (January – April 2016) seasons. A fox DNA blocking primer was designed to minimize the host amplicon products, and pooled samples were sequenced through paired-end reads (100 bp library) on a MiSeq Illumina Platform. The generated sequences were compared to a reference database built with sequences available in GenBank. In concordance with previous studies using traditional methods, we found that the most common food taxon were rodents. Qualitative differences in diet composition between both fox species were identified. Armadillo species were only found in pampas fox diet, while a greater variety of amphibians and birds were detected in crab-eating fox feces. Additionally, an innovative approach to differentiate between real and artifact sequences was employed. This method was based on comparing mutations at conserved and non-conserved positions within the secondary structure of the 12S rRNA, combined with network sequence reconstruction. Our results demonstrate the efficacy of the methodology in detecting the food species present in both fox diets, enabling the evaluation of intraspecific diversity among these species and facilitating the discarding of sequencing errors. This makes the methodology applicable to a wide range of studies.

Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.

To understand and manage any ecosystem, one of the most critical indicators is census population size (‘Nc’) for each component species. This is why the International Union for Conservation of Nature (IUCN) stipulates that it is ideal to know census size to an accuracy of ±10 % for each managed, endangered or exploited population. Knowledge of population size is also critical for: ecological studies in general; allowing biodiversity measures with low error margins; and assessing potential for evolutionary adaptation in long-term management. Unfortunately, despite their importance, all existing methods for estimating Nc have many difficulties, especially requiring independent knowledge or assumptions about demography, including: immigration, emigration, family size and its variance. As a result, even in the IUCN red list, many species are listed despite having unknown population size or trends. Therefore, we need an improved approach. This article introduces ‘DnaDot’, a strong new addition to our armory of census population size estimates, because it is an accurate estimate, with few assumptions. DnaDot is based on mark-release-recapture, but instead of marking, uses pre-existing polymorphisms to divide the population into separate groups. The method uses one sample, minimizing effort, uses no demographic assumptions or data, and does not require genotyping to be accurate enough to identify individuals and kin, which is problematic for other genetic methods especially when degraded field samples are used. DnaDot applies to any kind of variants, from tissue samples, or from noninvasive samples such as hair provided that the researcher can identify species-identity and variants within the species. DnaDot outperformed close competitors on minimal assumptions, and good detectability of marks. Also, in simulations of a wide range of scenarios, DnaDot had superior accuracy and precision, usually meeting the IUCN criterion of ±10 %, which competing methods rarely achieved. Finally, one other method is said to need smaller sample sizes than DnaDot, but only if that method is not required to meet the performance criteria of DnaDot.

Abstract Insects are essential not only for ecosystem functioning and food security but also comprise some of the world's most destructive invasive species. Therefore, both insect declines and invasions raise major conservation concerns globally and call for respective conservation or mitigation measures. However, studies of insects are hampered by intrinsic biological features of these organisms, which include extreme population fluctuations, a huge diversity of ecological strategies, and common cryptic species. Population genetics provides a large toolkit to adequately accommodate those features, thereby enabling researchers to inform and monitor the efficacy of conservation and mitigation programs. Here, we provide an overview of the molecular and analytical methods that are relevant to insect conservation or mitigation and highlight the challenges involved in their implementation. We detail how and why temporal changes in genetic diversity, population structure and migration, and the genetic basis of adaptation should be taken into account to inform insect management programs. Finally, we review the barriers to the broad adoption of population genetics in insect research and provide guidelines to facilitate the use of these methods by stakeholders. Overall, this review provides theoretical and practical guidelines for implementing population genetics in both insect conservation and control.

Russula griseocarnosa, an edible and medicinal mushroom abundant in nutrients and notable bioactivities, is predominantly grown in the broad-leaved forest with trees of the family Fagaceae in southern China. This species forms ectomycorrhizal associations with plant roots and cannot be artificially cultivated currently. Previous research indicates a strong correlation between the growth of R. griseocarnosa and factors such as the host plant, climate variables (specifically mean temperature and precipitation from June to October), and the rhizosphere microbiota of its habitat. However, comprehensive studies on the fundamental biology of this species are lacking. The interaction between R. griseocarnosa and its host plant, as well as the mechanisms underlying the microbial community dynamics within its habitat, remain ambiguous. The limited repertoire and diversity of carbohydrate-active enzymes (CAZymes) in R. griseocarnosa relative to saprophytic fungi may contribute to its recalcitrance to cultivation on synthetic media. The specific core enzyme and the substances provided by the host plant to facilitate growth are yet to be elucidated, posing a significant challenge in the artificial cultivation of R. griseocarnosa. The habitat of R. griseocarnosa harbours unique microbial communities, indicating the presence of potentially beneficial microorganisms that could be exploited for artificial propagation and conservation efforts. However, the lack of definitive functional verification experiments hinders the realization of this promising prospect. This review offers a comprehensive overview of the nutritional profile and health benefits of R. griseocarnosa, emphasizing recent developments in its isolation, molecular ecology, and artificial cultivation. Additionally, it explores prospective advancements in R. griseocarnosa research, aiming to enrich our foundational understanding for applied purposes and fostering progress in the realm of ectomycorrhizal edible mushrooms.

The introduction and subsequent range expansion of the American bullfrog (Lithobates catesbeianus) is part of a rising trend of troublesome biological invasions happening in China. This detrimental amphibious invasive species has strong adaptability. After its introduction and spread, it established its own ecological niche in many provinces of China, and its range has continued to expand to more areas. Previous studies recorded the introduction time of bullfrogs and calculated the changes in their genetic diversity in China using mitochondria, but the specific introduction route in China is still unknown. Expanding upon previous research, we employed whole-genome scans (utilizing 2b-RAD genomic sequencing) to examine single nucleotide polymorphisms (SNPs) and microsatellites within Lithobates catesbeianus to screen the genomes of these invasive amphibian species from eight Chinese provinces and two U.S. states, including Kansas, where bullfrogs originate. A total of 1,336,475 single nucleotide polymorphic loci and 17 microsatellite loci were used to calculate the genetic diversity of bullfrogs and their migration pathways. Our results suggest that the population in Hunan was the first to be introduced and to spread, and there may have been multiple introductions of subpopulations. Additionally, the genetic diversity of both the SNP and microsatellite loci in the Chinese bullfrog population was lower than that of the US population due to bottleneck effects, but the bullfrogs can adapt and spread rapidly. This study will offer crucial insights for preventing and controlling future introductions into the natural habitats in China. Additionally, it will assist in devising more precise strategies to manage the existing populations and curtail their continued expansion, as well as aim to improve clarity and originality while mitigating plagiarism risk.

Environmental and/or climate changes, occurring at a global or local scale, can significantly impact the diets, health, and population dynamics of waterbirds. This study aimed to develop an effective tool, using DNA metabarcoding of fecal samples, for monitoring waterbird diets during the breeding season in a Ramsar freshwater wetland in Northern France. We collected bird feces across eight marshes with varying anthropic usage. The majority of samples (69%) were from five waterbird species: Eurasian coot (Fulica atra), Eurasian moorhen (Gallinula chloropus), mallard (Anas platyrhynchos), mute swan (Cygnus olor), and grey heron (Ardea cinerea). DNA was extracted from 116 samples, with plant and invertebrate primers used to undertake multi-marker metabarcoding. Despite a negative impact of uric acid on DNA amplification, we observed significant dietary variations among bird species and sampling sites. Wetland bird diets primarily consisted of four arthropod families, dominated by Chironomidae and Asellidae. The number of plant families detected was higher, consisting of 33 families, with Poaceae highly prevalent within wetland bird diets. This study shows that using DNA metabarcoding to explore interactions between waterbirds and trophic resources is a promising approach to assist wetland management and assess the effect of environmental changes.

Background: Aedes aegypti, is the primary vector of dengue, Chikungunya, Zika, and yellow fever viruses. Both natural and human-impacted landscapes have selective pressures on Ae. aegypti, resulting in strong genomic structure even within close geographical distances. Materials and Methods: We assess the genetic structure of this medically important mosquito species at the northern leading edge of their distribution in Southwestern USA. Ae. aegypti were collected during 2017 in the urban communities of El Paso and Sparks, Texas (USA) and in the city of Ciudad Juárez, Mexico. Results: Thousands of nuclear loci were sequenced across 260 captured Ae. aegypti. First, we recovered the genetic structure of Ae. aegypti following geography, with all four major collection communities being genetically distinct. Importantly, we found population structure and genetic diversity that suggest rapid expansion through active-short distance dispersals, with Anapra being the likely source for the others. Next, tests of selection recovered eight functional genes across six outliers: calmodulin with olfactory receptor function; the protein superfamily C-type lectin with function in mosquito immune system and development; and TATA box binding protein with function in gene regulation. Conclusion: Despite these populations being documented in the early 2000s, we find that selective pressures on specific genes have already occurred and likely facilitate Ae. aegypti range expansion.

Black carp, Mylopharyngodon piceus , is one of the major farmed fish in China, generating a considerable amount of economic value annually. To investigate the genetic variation of black carp germplasm resources in China, this study was the first to use the whole genome SNPs of black carp for analysis. A total of 139 samples of nine black carp populations in the Yangtze River and Pearl River Systems of China were collected, and 53,322 high-quality SNP loci were obtained after GBS sequencing and filtering. Genetic diversity parameters were calculated for nine populations of black carp based on these genetic data. All 7 populations from the Yangtze River system and 2 populations from the Pearl River system showed high level of genetic diversity. For each population, the nucleotide diversity (π) varied from 0.283 to 0.308, the observed heterozygosity (H o) from 0.271 to 0.317, the expected heterozygosity (He) from 0.273 to 0.292，the number of effective alleles (Ne) from 1.440 to 1.475, and the polymorphism information content (PIC) from 0.224 to 0.239. The fixation index (F st) between populations ranged from 0.036 to 0.133, remaining at low and medium differentiation. Phylogenetic tree analysis, principal component analysis (PCA) and population genetic structure analysis revealed that the nine populations could be divided into three ancestral populations. The seven populations of the Yangtze River system comprised two primary ancestral groups, with a small amount of gene flow between populations. The internal genetic structure of populations within the Pearl River system was homogeneous, with one common ancestral source as the dominant component. In conclusion, the data and results generated from this study will provide a useful addition to the genetic resources of black carp and will provide reference information for further germplasm conservation and genetic improvement of black carp. • 53,322 high-quality SNP loci were obtained using Genotyping-by-sequencing technology. • High level of genetic diversity was in selected black carp populations. • Selected populations of black carp have low or medium genetic differentiation. • These black carp populations can be divided into three ancestral populations. [ABSTRACT FROM AUTHOR]

• Population sizes are crucial ecosystem indicators, but unfortunately very imperfect. • DnaDot adapts an old non-genetic measure for use with genetic marking of groups. • Repeat samples, many assumptions, and individual or kin ID are not needed. • Thus DnaDot avoids most pitfalls of previous population size estimates. • DnaDot performs well in comparison to older genetic and non-genetic measures. To understand and manage any ecosystem, one of the most critical indicators is census population size (' N c ') for each component species. This is why the International Union for Conservation of Nature (IUCN) stipulates that it is ideal to know census size to an accuracy of ±10 % for each managed, endangered or exploited population. Knowledge of population size is also critical for: ecological studies in general; allowing biodiversity measures with low error margins; and assessing potential for evolutionary adaptation in long-term management. Unfortunately, despite their importance, all existing methods for estimating N c have many difficulties, especially requiring independent knowledge or assumptions about demography, including: immigration, emigration, family size and its variance. As a result, even in the IUCN red list, many species are listed despite having unknown population size or trends. Therefore, we need an improved approach. This article introduces 'DnaDot', a strong new addition to our armory of census population size estimates, because it is an accurate estimate, with few assumptions. DnaDot is based on mark-release-recapture, but instead of marking, uses pre-existing polymorphisms to divide the population into separate groups. The method uses one sample, minimizing effort, uses no demographic assumptions or data, and does not require genotyping to be accurate enough to identify individuals and kin, which is problematic for other genetic methods especially when degraded field samples are used. DnaDot applies to any kind of variants, from tissue samples, or from noninvasive samples such as hair provided that the researcher can identify species-identity and variants within the species. DnaDot outperformed close competitors on minimal assumptions, and good detectability of marks. Also, in simulations of a wide range of scenarios, DnaDot had superior accuracy and precision, usually meeting the IUCN criterion of ±10 %, which competing methods rarely achieved. Finally, one other method is said to need smaller sample sizes than DnaDot, but only if that method is not required to meet the performance criteria of DnaDot. [ABSTRACT FROM AUTHOR]

Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)