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ABSTRACT True fungi ( Fungi ) and fungus-like organisms (e.g. Mycetozoa , Oomycota ) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

Although several studies have examined the functional diversity of freshwater macroinvertebrates, the variety of methodologies combined with the absence of a synthetic review make our understanding of this field incomplete. Therefore, we reviewed the current methodology for assessing functional diversity in freshwater macroinvertebrate research. Our review showed that most papers quantified functional diversity using biological traits, among which feeding habits were the most common traits probably due to the assumed links between feeding and ecosystem functions. A large number of diversity measures have been applied for quantifying functional diversity of freshwater macroinvertebrate assemblages, among which Rao’s quadratic entropy looks like the most frequent. In most papers, functional diversity was positively related to taxon richness, and functional redundancy was a key concept in explaining this correlation. Most studies detected strong influence of the environmental factors as well as human impact on functional diversity. Finally, our review revealed that functional diversity research is biased towards European running waters and is hindered by yet insufficient information on the autecology of macroinvertebrates.

Euarthropods owe their evolutionary and ecological success to the morphological plasticity of their appendages. Although this variability is partly expressed in the specialization of the protopodite for a feeding function in the post-deutocerebral limbs, the origin of the former structure among Cambrian representatives remains uncertain. Here, we describe Alacaris mirabilis gen. et sp. nov. from the early Cambrian Xiaoshiba Lagerstätte in China, which reveals the proximal organization of fuxianhuiid appendages in exceptional detail. Proximally, the post-deutocerebral limbs possess an antero-posteriorly compressed protopodite with robust spines. The protopodite is attached to an endopod with more than a dozen podomeres, and an oval flap-shaped exopod. The gnathal edges of the protopodites form an axial food groove along the ventral side of the body, indicating a predatory/scavenging autecology. A cladistic analysis indicates that the fuxianhuiid protopodite represents the phylogenetically earliest occurrence of substantial proximal differentiation within stem-group Euarthropoda illuminating the origin of gnathobasic feeding. The fuxianhuiids were a group of primitive true arthropods living in the Cambrian period. Here, Yang and colleagues describe a new species of fuxianhuiid, Alacaris mirabilis , from exceptionally-preserved specimens that illustrate the early evolution of specialized arthropod mouthparts.

Cannibalism, once viewed as a rare or aberrant behavior, is now recognized to be widespread and to contribute broadly to the self-regulation of many populations. Cannibalism can produce endogenous negative feedback on population growth because it is expressed as a conditional behavior, responding to the deteriorating ecological conditions that flow, directly or indirectly, from increasing densities of conspecifics. Thus, cannibalism emerges as a strongly density-dependent source of mortality. In this synthesis, we review recent research that has revealed a rich diversity of pathways through which rising density elicits increased cannibalism, including both factors that (a) elevate the rate of dangerous encounters between conspecifics and (b) enhance the likelihood that such encounters will lead to successful cannibalistic attacks. These pathways include both features of the autecology of cannibal populations and features of interactions with other species, including food resources and pathogens. Using mathematical models, we explore the consequences of including density-dependent cannibal attack rates on population dynamics. The conditional expression of cannibalism generally enhances stability and population regulation in single-species models but also may increase opportunities for alternative states and prey population escape from control by cannibalistic predators.

The mahseer fishes (Tor spp.) represent an iconic genus of large-bodied species of the Cyprinidae family. Across the 16 recognised species in the genus, individual fish can attain weights over 50 kg, resulting in some species being considered as premier sport fishes. Tor species also generally have high religious and cultural significance throughout South and Southeast Asia. Despite their economic and cultural importance, the status of Tor fishes has been increasingly imperilled through their riverine habitats being impacted by anthropogenic activities, such as hydropower dam construction and exploitation. Moreover, conservation efforts have been constrained by knowledge on the genus being heavily skewed towards aquaculture, with considerable knowledge gaps on their taxonomy, autecology, distribution and population status. Whilst taxonomic ambiguity has been a major constraint on conservation efforts, this has been partially overcome by recent, robust taxonomic revisions. This has enabled revision of the IUCN Red List status of Tor fishes; three species are now assessed as ‘Near Threatened’, one ‘Vulnerable’, three ‘Endangered’ and one ‘Critically Endangered’. However, eight species remain ‘Data deficient’. Here, information on these 16 Tor fishes is synthesised for the first time, outlining the current state of knowledge for each species, including their known distributions and population status. For each species, the outstanding gaps in knowledge are also identified, and their population threats and conservation prospects outlined. Consequently, this review provides the basis for researchers to challenge and enhance the knowledge base necessary to conserve these freshwater icons in an era of unprecedented environmental changes.

Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.

Modern ecological management problems are characterized by large scales, rapid environmental change, multiple stressors and conflicts between local and global conservation objectives. These problems are too complex to address with field studies alone, and statistical models that assume past system behaviours can predict future responses are risky when systems are changing rapidly. Mechanistic simulation models, though, can avoid that assumption while accommodating important natural complexities. Making mechanistic models credible requires empirical studies, but traditional study topics and designs often do not support them well. The models we use for modern problems need empirical studies that provide understanding of life history and autecology of study species, identify general patterns useful for model design and evaluation, collect data of kinds that models show are important and develop submodels and theory for individual‐level mechanisms. Ecologists can better produce such knowledge via research that: (a) is interdisciplinary and across‐level, often designed to understand just enough about individuals to support individual‐based models of populations and communities; (b) is designed to quantify relationships across broad ranges, instead of testing statistical hypotheses; (c) emphasizes relevance and realism over precision; and (d) includes stressful conditions relevant to modern management challenges. Supporting complex management models is rewarding to research ecologists: Modelling identifies crucial yet understudied research topics; models can be used as virtual ecosystems for experiments (including tests of theory) that would be impossible in reality; and supporting models ensures that our work has high impact and contributes to critical issues.

The New Zealand mud snail (Potamopyrgus antipodarum; NZMS) is among the most globally widespread aquatic invaders, occurring in 39 countries and 5 continents. Herein we provide a systematic review of 245 articles, focusing on the ecological impacts, spatial distribution, population dynamics, vectors of spread, and management of invasive NZMS. Most NZMS introductions originate from already-established invasive populations, which represent a small number of clonal lineages. The invasion success of NZMS stems from opportunistic traits, and while their tolerance of broad ranges of environmental conditions facilitates spread, optimal conditions for successful NZMS establishment are evident: stable hydrology, slow water velocity, high specific conductivity, and moderate salinity. NZMS can become exceptionally abundant, driving the greatest secondary-production rates reported for any stream invertebrate. However, NZMS populations fluctuate seasonally and over longer time scales, with marked declines observed after population booms. Minimal genetic variation within and among invasive populations and minimal incidences of predation/parasitism suggest that environmental factors constrain populations. As detritivore-herbivores, NZMS impact multiple compartments of aquatic ecosystems and their functioning. NZMS alter invertebrate and algal communities and can resist digestion by many fish species, reducing fish condition. This lack of digestion combined with expanding NZMS populations suggest that snail-eating fish are unlikely to regulate NZMS populations and may aid in local range expansion. Management programs and technologies have recently emerged to assist resource managers, including advances in environmental DNA detection methods and effective chemical decontamination treatments. The objective of this review is to contribute to a more robust understanding of the global NZMS invasion, such that undesired impacts can be minimized or averted.

Aim Cetaceans are inherently difficult to study due to their elusive, pelagic and often highly migratory nature. New Zealand waters are home to 50% of the world's cetacean species, but their spatial distributions are poorly known. Here, we model distributions of 30 cetacean taxa using an extensive at‐sea sightings dataset (n > 14,000) and high‐resolution (1 km2) environmental data layers. Location New Zealand's Exclusive Economic Zone (EEZ). Methods Two models were used to predict probability of species occurrence based on available sightings records. For taxa with <50 sightings (n = 15), Relative Environmental Suitability (RES), and for taxa with ≥50 sightings (n = 15), Boosted Regression Tree (BRT) models were used. Independently collected presence/absence data were used for further model evaluation for a subset of taxa. Results RES models for rarely sighted species showed reasonable fits to available sightings and stranding data based on literature and expert knowledge on the species' autecology. BRT models showed high predictive power for commonly sighted species (AUC: 0.79–0.99). Important variables for predicting the occurrence of cetacean taxa were temperature residuals, bathymetry, distance to the 500 m isobath, mixed layer depth and water turbidity. Cetacean distribution patterns varied from highly localised, nearshore (e.g., Hector's dolphin), to more ubiquitous (e.g., common dolphin) to primarily offshore species (e.g., blue whale). Cetacean richness based on stacked species occurrence layers illustrated patterns of fewer inshore taxa with localised richness hotspots, and higher offshore richness especially in locales of the Macquarie Ridge, Bounty Trough and Chatham Rise. Main conclusions Predicted spatial distributions fill a major knowledge gap towards informing future assessments and conservation planning for cetaceans in New Zealand's extensive EEZ. While sightings datasets were not spatially comprehensive for any taxa, these two best available approaches allow for predictive modelling of both more common, and of rarely sighted, cetacean species with limited available information.