Gotowa bibliografia na temat „Trait abundance distribution”

Background Community assembly by trait selection (CATS) allows for the detection of environmental filtering and estimation of the relative role of local and regional (meta-community-level) effects on community composition from trait and abundance data without using environmental data. It has been shown that Poisson regression of abundances against trait data results in the same parameter estimates. Abundance data do not necessarily follow a Poisson distribution, and in these cases, other generalized linear models should be fitted to obtain unbiased parameter estimates. Aims This paper discusses how the original algorithm for calculating the relative role of local and regional effects has to be modified if Poisson model is not appropriate. Results It can be shown that the use of the logarithm of regional relative abundances as an offset is appropriate only if a log-link function is applied. Otherwise, the link function should be applied to the product of local total abundance and regional relative abundances. Since this product may be outside the domain of the link function, the use of log-link is recommended, even if it is not the canonical link. An algorithm is also suggested for calculating the offset when data are zero-inflated. The relative role of local and regional effects is measured by Kullback-Leibler R2. The formula for this measure presented by Shipley (2014) is valid only if the abundances follow a Poisson distribution. Otherwise, slightly different formulas have to be applied. Beyond theoretical considerations, the proposed refinements are illustrated by numerical examples. CATS regression could be a useful tool for community ecologists, but it has to be slightly modified when abundance data do not follow a Poisson distribution. This paper gives detailed instructions on the necessary refinement.

Ecologists widely accept that the distribution of abundances in most communities is fairly flat but heavily dominated by a few species. The reason for this is that species abundances are thought to follow certain theoretical distributions that predict such a pattern. However, previous studies have focused on either a few theoretical distributions or a few empirical distributions. I illustrate abundance patterns in 1055 samples of trees, bats, small terrestrial mammals, birds, lizards, frogs, ants, dung beetles, butterflies, and odonates. Five existing theoretical distributions make inaccurate predictions about the frequencies of the most common species and of the average species, and most of them fit the overall patterns poorly, according to the maximum likelihood–related Kullback-Leibler divergence statistic. Instead, the data support a low-dominance distribution here called the “double geometric.” Depending on the value of its two governing parameters, it may resemble either the geometric series distribution or the lognormal series distribution. However, unlike any other model, it assumes both that richness is finite and that species compete unequally for resources in a two-dimensional niche landscape, which implies that niche breadths are variable and that trait distributions are neither arrayed along a single dimension nor randomly associated. The hypothesis that niche space is multidimensional helps to explain how numerous species can coexist despite interacting strongly.

Abstract The goal of this study was to use BxD recombinant inbred mice to search for genes that control the hypothalamic corticotrophin-releasing factor (CRF) system. The specific phenotype that was measured was abundance of transcripts that encode CRF, CRF receptor (Crf-R1), CRF binding protein, and arginine vasopressin (AVP) in total hypothalamic RNA. The strain distribution patterns for the transcript abundances for each target were continuously distributed, consistent with these being quantitative traits. Marker regression and interval mapping revealed associations with quantitative trait loci (QTL) for CRF transcript abundance on chromosome 1 (at 89.2 cM), chromosome 12 (between 54–58 cM), and chromosome 13 (between 26–30 cM); for Crf-R1 transcript abundance on chromosome 7 (at 1.5 cM), chromosome 12 (at 37 cM), and chromosome X (at 30 cM); for CRF binding protein transcript abundance on chromosome 7 (at 48.5 cM), chromosome 8 (at 65 cM), and chromosome 12 (at 19 cM); and for AVP transcript abundance on chromosome 7 (at 1 cM), chromosome 12 (at 13 cM), and chromosome 13 (at 45 cM). The transcript abundance QTL were not linked to their respective structural genes. Interval mapping on chromosome 7 reveals substantial overlap between QTL that control AVP and Crf-R1 transcript abundance and on chromosome 12 for QTL that control CRF and Crf-R1, which may indicate loci that coordinate regulation of the CRF system. There are QTL for all four targets on chromosome 12. There are a number of neurodevelopmental genes in very close proximity to the transcript abundance QTL that are potential candidate genes.

Abstract Copepods are the dominant marine zooplankton and perform important functions in the marine food web. However, copepod traits have not been studied in many waters. We studied the copepod community under influence of the Mekong River and the Southern Vietnamese coastal upwelling, based on their functional traits, during the southwest monsoon period in 2016. Fourteen trait categories of four key functional traits (trophic-groups, feeding-types, reproductive-strategies and diel migration) of copepod data were analyzed to investigate how environmental gradients impact on their distribution and abundance among the four defined habitats: Mekong River (MKW), upwelling (UpW), nearshore (OnSW) and offshore waters (OSW). There were seven functional groups identified in the study waters based on multiple correspondence analysis of distribution, abundance and traits of 139 copepod species. Herbivorous, current-feeding and sac-spawning copepods were dominant in all habitats with the highest abundance in OSW. Specifically, herbivorous species dominated in MKW and UpW, whereas omnivorous species dominated in OnSW and OSW. Sac-spawners dominated in all habitats, but decreased from MKW and UpW to OnSW and lowest in OSW. Cruise feeders were 2-fold higher than ambush feeders in the UpW, but the opposite was observed in the other habitats. The results suggest that impacts of Mekong River and coastal upwelling led to distinctive copepod assemblages with specific functional traits.

Abstract. Declines in species richness and abundance of insects over the last decades are often driven by anthropogenic land use and can have severe consequences for ecosystem functioning. Many studies investigated the effects of land-use intensification on the distribution of phenotypic traits across species at the community level, often with mixed results. However, biotic and abiotic environmental filters and potential selection act on individuals within each species, i.e., at the species' population level, and thus drive the extent of intraspecific phenotypic variation. Here, we compare the morphological trait variation within selected species of dung beetles, bees and grasshoppers and link this variation to land-use intensity in forests and grasslands. Selected traits included absolute body size measures and relative leg, wing or eye size, or shape and are often interpreted as “functional traits” in the context of specific ecological responses or effects. We predicted that trait variability among individuals of arthropod species is reduced in intensively used ecosystems (with pronounced environmental filtering) compared to low-intensity ones, particularly for arthropod species that were more abundant in intensively used sites (“land-use winners” compared to “losers”). In general, only few effects of land-use intensity on trait variation were found showing a decreasing variation with increasing land-use intensity in forests but an increasing variation in grasslands. Although many studies confirmed strong land-use impacts on species composition, diversity and trait distribution, including evidence from the same land-use gradients, we were not able to confirm consistent effects at the intraspecific level. However, the choice of which traits are included in analyses and the linkage between phenotypic variation and genetic variability can strongly influence the conclusions drawn on ecological processes. Therefore, we suggest extending the use of intraspecific trait variation on other, more specific response or effect traits and a broader range of species in future studies.

A principal goal in ecology is to identify the determinants of species abundances in nature. Body size has emerged as a fundamental and repeatable predictor of abundance, with smaller organisms occurring in greater numbers than larger ones. A biogeographic component, known as Bergmann’s rule, describes the preponderance, across taxonomic groups, of larger-bodied organisms in colder areas. Although undeniably important, the extent to which body size is the key trait underlying these patterns is unclear. We explored these questions in diatoms, unicellular algae of global importance for their roles in carbon fixation and energy flow through marine food webs. Using a phylogenomic dataset from a single lineage with worldwide distribution, we found that body size (cell volume) was strongly correlated with genome size, which varied by 50-fold across species and was driven by differences in the amount of repetitive DNA. However, directional models identified temperature and genome size, not cell size, as having the greatest influence on maximum population growth rate. A global metabarcoding dataset further identified genome size as a strong predictor of species abundance in the ocean, but only in colder regions at high and low latitudes where diatoms with large genomes dominated, a pattern consistent with Bergmann’s rule. Although species abundances are shaped by myriad interacting abiotic and biotic factors, genome size alone was a remarkably strong predictor of abundance. Taken together, these results highlight the cascading cellular and ecological consequences of macroevolutionary changes in an emergent trait, genome size, one of the most fundamental and irreducible properties of an organism.

Recent studies have renewed interest in sponge ecology by emphasizing the functional importance of sponges in a broad array of ecosystem services. Many critically important habitats occupied by sponges face chronic stressors that might lead to alterations in their diversity, relatedness, and functional attributes. We addressed whether proximity to human activity might be a significant factor in structuring sponge community composition, as well as potential functional roles, by monitoring sponge diversity and abundance at two structurally similar sites that vary in distance to areas of high coastal development in Bocas Del Toro, Panama. We surveyed sponge communities at each site using belt transects and differences between two sites were compared using the following variables: (1) sponge species richness, Shannon diversity, and inverse Simpson’s diversity; (2) phylogenetic diversity; (3) taxonomic and phylogenetic beta diversity; (4) trait diversity and dissimilarity; and (5) phylogenetic and trait patterns in community structure. We observed significantly higher sponge diversity at Punta Caracol, the site most distant from human development (∼5 km). Although phylogenetic diversity was lower at Saigon Bay, the site adjacent to a large village including many houses, businesses, and an airport, the sites did not exhibit significantly different patterns of phylogenetic relatedness in species composition. However, each site had a distinct taxonomic and phylogenetic composition (beta diversity). In addition, the sponge community at Saigon included a higher relative abundance of sponges with high microbial abundance and high chlorophyllaconcentration, whereas the community at Punta Caracol had a more even distribution of these traits, yielding a significant difference in functional trait diversity between sites. These results suggest that lower diversity and potentially altered community function might be associated with proximity to human populations. This study highlights the importance of evaluating functional traits and phylogenetic diversity in addition to common diversity metrics when assessing potential environmental impacts on benthic communities.

Although the effects of introduced predators on prey populations in aquatic ecosystems have been studied frequently, less is known about the interactions between predators. We performed a whole-lake experiment by stocking a non-native top predator (pikeperch (Sander lucioperca)) to two residential piscivores (Eurasian perch (Perca fluviatilis) and northern pike (Esox lucius)). By analyzing spatial distribution, diet composition, growth, and consumption rates of the piscivores before and after pikeperch introduction, we tested how both density-dependent and trait-mediated responses affected interactions between the three predators. Total piscivore biomass increased 1.5 times and annual consumption by the piscivores increased 1.7 times after stocking, attributable to the stocked pikeperch and increased northern pike abundances. Abundance, distribution, and consumption data indicated that northern pike was hardly affected by pikeperch stocking and even increased its biomass, whereas piscivorous perch shifted its habitat use towards the littoral lake areas in response to competition with pikeperch. Furthermore, all piscivores increasingly fed on small perch. The forced habitat shift of piscivorous perch in combination with increased predation on small perch led to a decreased abundance of large perch, attributable to the compensatory effects of intraguild predation and cannibalism.

Functional trait-based approaches provide an opportunity to assess how changes in habitat affect the structure of associated communities. Global analyses have found a similarity in the composition of reef fish functional traits despite differences in species richness, environmental regimes, and habitat components. These large-scale patterns raised the question of whether this same stability can be observed at smaller spatial scales. Here, we compared the fish trait composition and their functional diversity in two Caribbean shallow coral reefs with contrasting levels of habitat degradation: Limones (>30% cover), constituted mainly by colonies of Acropora palmata and Bonanza, a reef with extensive areas of dead Acropora structures, dominated by algae. To characterize the functional structure of fishes on each reef, we calculated the community-weighted mean trait values (CWM), functional richness, functional evenness, functional dispersion, and functional originality. Despite the differences in habitat quality, reefs exhibited a similar proportion and common structure on fish functional traits. Functional richness and functional evenness differed significantly, but functional dispersion and functional originality did not show differences between reefs. The greater niche complexity driven by the high availability of microhabitats provided by A. palmata may explain the higher functional richness in Limones, whereas the reef degradation in Bonanza may contribute to a higher functional evenness because of a similar distribution of abundance per fish trait combinations. Our results suggest that widespread degradation on Caribbean reefs has limited the type, variety, and range of traits, which could lead to a functional homogenization of fish communities even at local scales.

Comprendre et prédire la dynamique de la biodiversité sous contraintes du changement global représente un défi scientifique majeur. Cependant, la réponse de la biodiversité au changement global est intrinsèquement complexe. En effet, les facteurs de changement en jeu n'affectent pas seulement la diversité des espèces et leur abondance, mais modifient également les interactions biotiques entre espèces, ce qui impacte l‘assemblage des communautés et leurs dynamiques. Dans ce contexte, l'étude de la diversité des traits fonctionnels pourrait permettre des avancées significatives car les traits reflètent la manière dont les espèces répondent et influencent leur environnement. Pour rendre l'approche fonctionnelle opérationnelle à l'étude de la complexité des systèmes écologiques, nous avons développé une démarche analytique novatrice qui repose sur l'étude des formes de distribution de traits. La forme des distributions de traits peut être caractérisée par une la relation entre la skewness et la kurtosis : la SKR. Plus précisément, nous avons développé deux indicateurs clés (Chapitre 1), dérivés de la SKR : le TADeve qui caractérise l'équitabilité fonctionnelle, et le TADstab qui caractérise la stabilité des distributions de traits.En nous appuyant sur les prairies permanentes comme modèle d'étude, nous avons mis en avant la pertinence de l'étude de l'équitabilité (TADeve) et de la stabilité (TADstab) des distributions de traits afin de dissocier l'influence de processus déterministes (p.ex. filtre de l'habitat, différentiation de niche) de la stochasticité inhérente aux systèmes écologiques (Chapitre 1). La mobilisation d'un jeu de données de suivi de prairies permanentes gérées de manière contrastée sur le long terme (17 ans), nous a permis de montrer que la dynamique des distributions de traits n'était pas aléatoire mais dépendante des pratiques de gestion (Chapitre 2). Les prairies gérées de manière intensive (haut niveau de fertilisation) sont associées à des distributions de traits instables et inéquitables. Ces résultats sont cohérents avec un scénario théorique du « filtre de l'habitat » et l'effet d'une compétition intense limitant la diversité. Dans le cas des prairies gérées de manière extensive (absence de fertilisation), les distributions de traits sont remarquablement équitables et stables. Ces résultats sont cohérents avec un scénario théorique de la « différenciation de niche » prédisant une coexistence stable d'espèces fonctionnellement contrastées. Par ailleurs, nous avons montré que l'arrêt de la fertilisation entraîne, en quelques années, une convergence vers des distributions de traits équitables et stables, favorisant ainsi le recrutement à long terme d'une flore prairiale riche et diversifiée. Nous montrons également que l'équitabilité et la stabilité des distributions de traits s'expliqueraient par l'émergence d'une complémentarité entre espèces dominantes et subordonnées permettant une stabilisation sur le long terme de l'assemblage fonctionnel et de toute la communauté végétale (Chapitre 3). Enfin, une étude comparative des patrons de diversité fonctionnelle, entre des communautés prairiales gérées et des communautés végétales naturelles, nous a permis de montrer que ces communautés partagent des organisations fonctionnelles similaires. L'observation de patrons communs dans le temps et dans l'espace suggère l'existence de règles générales déterminant à la fois l'assemblage, la diversité et la dynamique des communautés prairiales.En conclusion, l'approche SKR semble adaptée à l'étude de systèmes complexes dynamiques, tels que les systèmes écologiques en contexte de changement global. A l'ère de l'anthropocène, l'identification de règles générales d'assemblage basées sur les traits permettrait de concevoir des modes de gestion adaptés à la préservation et à la restauration de la biodiversité, ainsi qu'au maintien de la multifonctionnalité des écosystèmes
Understanding and predicting the dynamics of biodiversity under global change is a major scientific challenge. However, biodiversity responses to global change are inherently complex. Drivers of change not only affect species diversity and abundance but also alter biotic interactions between species, which may impact community assembly and dynamics. In this context, studying the diversity of functional traits within communities could lead to significant advances, as traits reflect how species respond to and influence their environment. To make the trait-based approach operational for the study of complex ecological systems, we developed an innovative analytical framework based on the study of the shapes of trait distributions. The shapes of trait distributions can be characterised by an inequality between the skewness and the kurtosis, the Skewness-Kurtosis Relationship (SKR). Using this inequality, we developed two key indicators (Chapter 1): the TADeve, which characterises the evenness of trait distributions, and the TADstab, which characterises the stability of trait distributions.Using permanent grasslands as a study model, we highlighted the relevance of studying the evenness (TADeve) and stability (TADstab) of trait distributions in order to disentangle the influence of deterministic processes (e.g. habitat filtering, niche differentiation), while accounting for the inherent stochasticity of ecological systems (Chapter 1). Using a long-term dataset of managed permanent grasslands (17-years), we demonstrated that the temporal variability of trait distributions was not random, but depended on management practices (Chapter 2). Intensively managed grasslands (high levels of fertilisation) are associated with unstable and uneven trait distributions. These results are consistent with predictions of the “habitat filtering” theory and the occurrence of intense competition between plant species that limit local diversity. Conversely, extensively managed grasslands (no fertilisation) were linked to remarkably even and stable trait distributions over time. Furthermore, we also showed that the cessation of fertilisation in extensively-managed grasslands led to a rapid convergence towards even and stable trait distributions, which promoted the long-term recruitment and persistence of a rich and diverse grassland flora. These findings are consistent with a theoretical scenario of niche differentiation, which predicts a stable coexistence among functionally contrasting species. Finally, we found that the high evenness and stability of trait distributions, in extensively managed grasslands, are explained by a functional complementarity between dominant and subordinate species, facilitating the long-term stabilisation of the functional assemblage and of the entire plant community (Chapter 3). Using observational data from various ecological context, we showed that semi-natural and natural plant communities shared a similar functional organisation. The observation of common functional patterns over space and time suggests the existence of general rules governing the assembly, diversity, and dynamics of plant communities.In conclusion, the SKR approach appears to be a suitable tool to study complex dynamic systems, such as ecological systems in the context of global change. In the Anthropocene era, identifying general assembly rules based on functional traits could enable the design of management methods adapted to the conservation and restoration of biodiversity, as well as the maintenance of ecosystem multifunctionality

Black bears are omnivorous, and tend to be opportunistic feeders, in that they will eat what is readily abundant or available. The end-products of intestinal digestion are absorbed by the body through the action of transporter proteins expressed on the brushborder membrane of small intestinal epithelial cells. The goal of this study was to increase the understanding of the physiological processes associated with nutrient assimilation by black bears. Distribution and relative abundance of mRNA of a peptide transporter (PepT1), a glucose transporter (SGLT1), two AA transporters (NBAT, bo,+AT), and a digestive enzyme, aminopeptidase N (APN), in the intestinal tract of black bears were investigated. Ten bears were used for this study. For tissue collection, the intestine was removed from the animal and divided into five sections. Each collected section was opened longitudinally, rinsed in ice-cold PBS, and the mucosal scrapings were stored at -80C. Total RNA was extracted and quantified by spectrophotometry. Abundance of PepT1, SGLT1, NBAT, bo,+AT, and APN mRNA was determined by performing Northern blots, using bear cDNA probes. Northern blot data were quantified by densitometric analysis, with the abundance of each gene expressed relative to GAPDH. Abundance of PepT1 (P < 0.05), APN (P < 0.05), and SGLT1 (P < 0.0001) changed quadratically from the proximal to the distal intestine with abundance being greatest in the midregion. Abundance of bo,+AT mRNA increased linearly (P < 0.05) from the proximal to distal intestine. Abundance of NBAT mRNA did not change among intestinal segments.The absolute number of molecules of mRNA/ng of total RNA for each gene was determined using Real-Time PCR. Similar to the Northern results, abundance of PepT1 (P < 0.0003), SGLT1 (P < 0.0003), and APN (P < 0.02) changed quadratically from the proximal to distal intestine with abundance being greatest in the mid-region, and bo,+AT mRNA increased linearly (P < 0.0001) from the proximal to distal intestine. NBAT mRNA abundance also increased linearly (P < 0.0001) from proximal to distal intestine. PepT1 mRNA was present at tenfold or greater levels than AA transporter mRNA in all segments of the intestine, suggesting that di- and tripeptides constitute the major form in which AAs are absorbed. NBAT and bo,+AT mRNA abundance was greater towards the distal portion of the intestine, suggesting their importance in salvaging remaining unabsorbed AAs.These results indicate that the mRNA of nutrient transporters examined and APN are differentially expressed throughout the gastrointestinal tract of black bears, suggesting their involvement in nutrient assimilation.
Master of Science

Ash dieback is a severe disease of ash trees (Fraxinus spp.), caused by the invasive fungus Hymenoscyphus fraxineus. In its native East Asia, H. fraxineus is a harmless endophyte, but since its accidental import into Europe in the early 1990s it has infected over 90% of ash trees in some areas, with long-term mortality sometimes exceeding 90%. The disease was discovered in Great Britain in 2012, and has since spread rapidly. This thesis investigates some of the possible impacts on biodiversity, ecosystem functioning, and society, and in doing so identifies ways to alleviate some impacts. Britain has only 13% tree cover (among the lowest in Europe), so may be particularly vulnerable to ash loss. Better understanding of the effects and how to minimise them is critical to deliver an evidence-based response. First, we investigated impacts in woodlands by experimentally killing woodland ash trees by ring-barking. We found no short-term effect of ash loss on ground flora or earthworm communities, or on the regeneration or growth of other woody species. Observational evidence suggested that remaining canopy trees rapidly filled gaps left by ash, perhaps contributing to stability. Our woodlands appeared to be remarkably resilient to ash loss, although there may be long-term effects or impacts on other species that this experiment failed to observe. To investigate broader-scale impacts, we required high-quality abundance maps for ash and other trees across Britain. Using species distribution modelling and random forest regression, we developed a protocol to produce abundance maps from readily available data. We tested the predictive power of the resulting maps using cross validation. Our maps are the best available for abundance of British tree species, and will be useful across a wide range of disciplines. We then used them to model ecosystem vulnerability to ash loss, based on the abundance of ash and other tree species, and their ecological trait similarity. We identified areas at risk of the largest impacts, and produced guidance for positive management actions to minimise ecological change. Lastly, we investigated the financial impacts of ash dieback, estimating the total cost to Britain at £9.2 billion. This figure is many times larger than the value of lost trade if biosecurity were improved to prevent future invasions, questioning the validity of financial arguments against biosecurity. We also found that loss of ecosystem services accounted for less than a third of the total cost, suggesting that ecosystem service assessments may miss a large proportion of the true cost of biodiversity loss. Overall, we found that some impacts may be less than expected, such as local effects on woodland ground flora, and others, such as the economic cost, may be much larger than expected. However, the resilience of ecosystems to a major shock such as loss of a common species, and actions to mitigate the impacts, depend on having a diversity of other trees present. The ash dieback outbreak highlights the importance of preventing other severe pests and diseases of trees from being introduced; something that has been increasing exponentially, largely due to international trade in trees. This thesis provides further firm evidence that there is an ecological and social imperative to halt this trend.

AbstractThe oceanic islands of the Gulf of Guinea (Príncipe, São Tomé, and Annobón) are an exceptional centre of endemism for flora and fauna. Remarkable progress has been made in biological research during the last few decades: from species being described and reported for the first time, to general patterns of species-habitat associations found across terrestrial, coastal, and marine taxa. Despite this increase in knowledge, key aspects of Gulf of Guinea species ecology remain poorly understood. This chapter reviews existing knowledge on the biodiversity of the islands, focusing on species distributions, population abundance estimates, traits, habitat associations and interactions. To promote these islands as ecological models, and to ensure the future of their endemic-rich biodiversity, it is essential to overcome current knowledge gaps and reduce existing taxonomic, spatial, and temporal biases in the information available. Therefore, future studies should favour systematic island-wide surveys and prioritize understudied areas and taxonomic groups. Moreover, long-term monitoring studies are urgently needed to assess biodiversity trends and to advise conservation actions. The future of ecological research and conservation of the unique biodiversity of these islands must increasingly rely on the development of local biodiversity-focused scientific expertise, through outreach, capacity building, and advanced training, paired with international collaborations and the development of local organizations.

Abstract For almost all butterflies, oviposition preference is the principal mechanism by which the insect-host plant relationship is established. It is this trait of the insect that interacts with spatial distributions, abundances, and acceptabilities of plants to generate patterns of insect-host association across the landscape. There are a few putative exceptions. Parnassius apollo in Sweden and Melanargia galathea in Britain are described as scattering eggs without regard to host distributions (Ford 1945, Wiklund 1982). Nonetheless, all aspects of the distribution and abundance of butterflies are influenced by host plant relations.

This chapter calculates the abundance (or biomass) of all species in a community as a function of their asymptotic size. It develops a purely analytical theory of the asymptotic size trait distribution in a fish community. The theory is based upon the Sheldon community spectrum developed in Chapter 2, and the new theory is used here to formulate an “extended” Sheldon conjecture. The analytic theory describes only a steady-state solution, which is of limited use for impact assessments of fishing; that requires a dynamic trait-based size spectrum model, which is next developed. To conclude, the chapter demonstrates how the trait-based model can be extended to model specific stocks embedded in a food web.

This chapter focuses on the ecological and evolutionary principles of marine biology. It starts with the definition of ecology, which is the study of interactions between organisms and their environment and the effects of these interactions on the distribution and abundance of organisms. The ecological hierarchy consists of the individual, population or species, community, ecosystem, and biosphere. Meanwhile, community ecology helps determine the distributions of how species alter their habitat to allow others to live there. The chapter considers direct interactions among species in an ecosystem, such as competition and predation. It mentions how natural selection can result in changes in traits that vary in function of genetic polymorphism and plasticity.

Abstract One of the most urgent concerns in global biodiversity conservation is the impact of changing climate on insect pollinator biology and pollination. This chapter reviews the impacts of warmer temperatures, drought, enriched carbon dioxide and extreme weather events on insect pollinators, their plant food resources and potential shifts in their species interactions, including trait, temporal and spatial mismatches, with implications for functional change. We posit that the direct effects of climate change on the physiology, traits, phenology, abundance and distributions of insect pollinators and their plant food resources are far better understood than the indirect effects of climate on plant–pollinator interactions. Further, the functional consequences of climate-induced changes for plant pollination remain understudied, and even less is known about fitness consequences of interaction mismatches for insect pollinators.

The degradation of surface water by anthropogenic activities is a global phenomenon. Surface water in the upper Crocodile River has been deteriorating over the past few decades by increased anthropogenic land use and land cover changes as areas of non-point sources of contamination. This study aimed to assess the spatial variation of physicochemical parameters and potentially toxic elements (PTEs) contamination in the Crocodile River influenced by land use and land cover change. 12 surface water samplings were collected every quarter from April 2017 to July 2018 and were analyzed by inductive coupled plasma spectrometry-mass spectrometry (ICP-MS). Landsat and Spot images for the period of 1999–2009 - 2018 were used for land use and land cover change detection for the upper Crocodile River catchment. Supervised approach with maximum likelihood classifier was used for the classification and generation of LULC maps for the selected periods. The results of the surface water concentrations of PTEs in the river are presented in order of abundance from Mn in October 2017 (0.34 mg/L), followed by Cu in July 2017 (0,21 mg/L), Fe in April 2017 (0,07 mg/L), Al in July 2017 (0.07 mg/L), while Zn in April 2017, October 2017 and April 2018 (0.05 mg/L). The concentrations of PTEs from water analysis reveal that Al, (0.04 mg/L), Mn (0.19 mg/L) and Fe (0.14 mg/L) exceeded the stipulated permissible threshold limit of DWAF (< 0.005 mg/L, 0.18 mg/L and 0.1 mg/L) respectively for aquatic environments. The values for Mn (0.19 mg/L) exceeded the permissible threshold limit of the US-EPA of 0.05 compromising the water quality trait expected to be good. Seasonal analysis of the PTEs concentrations in the river was significant (p > 0.05) between the wet season and the dry season. The spatial distribution of physicochemical parameters and PTEs were strongly correlated (p > 0.05) being influenced by different land use type along the river. Analysis of change detection suggests that; grassland, cropland and water bodies exhibited an increase of 26 612, 17 578 and 1 411 ha respectively, with land cover change of 23.42%, 15.05% and 1.18% respectively spanning from 1999 to 2018. Bare land and built-up declined from 1999 to 2018, with a net change of - 42 938 and − 2 663 ha respectively witnessing a land cover change of −36.81% and − 2.29% respectively from 1999 to 2018. In terms of the area under each land use and land cover change category observed within the chosen period, most significant annual change was observed in cropland (2.2%) between 1999 to 2009. Water bodies also increased by 0.1% between 1999 to 2009 and 2009 to 2018 respectively. Built-up and grassland witness an annual change rate in land use and land cover change category only between 2009 to 2018 of 0.1% and 2.7% respectively. This underscores a massive transformation driven by anthropogenic activities given rise to environmental issues in the Crocodile River catchment.

The field of weed ecology involves the examination of growth characteristics, adaptive traits, and survival mechanisms of weeds that allow them to effectively utilize environmental resources and successfully establish themselves in new habitats. The analysis of the ecological and biological characteristics of weeds enhances our understanding of the relationships between weeds and crops, as well as the factors contributing to their widespread establishment and management strategies. Climate, soil conditions, and biotic factors affect their geographic distribution, abundance, competitive abilities, behavioral tendencies, and survival. Despite the challenges posed by environmental factors and human interventions, weeds have a remarkable capacity to flourish and persist across many ecosystems. Several reasons may contribute to this phenomenon, including seed production in vast quantities, variable seed dormancy and longevity, propagation through vegetative organs, and mimicking the appearance of the crop.

India’s alluvial plains once supported the abundance of greater one-horned rhino (Rhinoceros unicornis; hereafter rhino). Due to uncontrolled poaching and land degradation due to human intervention, they lost almost 80% of their natural habitat. Around 90% of rhinos are confined to Assam, along the Gangetic plains in northeastern India. Having formerly been a habitat for Indian rhinos, Uttar Pradesh reintroduced them at Dudhwa National Park in 1984. Based on secondary data collected from the study area (1984–2021), we analyzed the rhino population\'s life-history traits. Seven rhinos were brought from Assam and Nepal to start the seed population, including two males and five females. The rhino population increased steadily in the Dudhwa NP and reached asymptote. Birth rate and mortality rate were 0.17/year and 0.05/year, respectively. Observation of 10 adult females over 47 birth records revealed a higher fertility rate between 8 and 20 years, with a mean inter-birth interval of 4.3 years. According to their large body size, rhinos exhibit similar life-history traits to other large mammals, such as a slow onset of sexual maturity, few young, high inter-birth intervals, and fertility into old age. The current estimated population of Indian rhinoceros is about 35–40 in Uttar Pradesh.

Pseudotsuga menziesii ((Mirb.) Franco), known as Douglas fir, is a prominent conifer species native to North America. It is known for its adaptability, rapid growth, and high-quality wood. It was introduced to Europe in the nineteenth century and is currently the most abundant non-native tree species cultivated in Central European forests. In Portugal, the species was initially cultivated as an ornamental plant and used for experimental purposes. However, its notable qualities, particularly its high volume production, have garnered significant interest. This has led to the implementation of reforestation programs, which expanded the forested areas by the late twentieth century. This study aims to review the state-of-the-art on the species, with a focus on forest stands outside its natural distribution area, specifically in Portugal. The authors present information on the species’ traits, growth dynamics, silviculture and management, available models to support its management, and wood properties. The main specific areas covered are: (i) the botanical and ecological characteristics of the species, including its distribution, genetic diversity, and responses to biotic and abiotic stresses; (ii) silvicultural practices and management strategies adapted to the species in Portugal, along with an overview of models and decision support tools; and (iii) characteristics of wood, covering its biometry, physical and mechanical properties.

Sometimes referred to as the “great unseen,” microbes (e.g., bacteria, fungi, protists) are by far the most abundant organisms on Earth. Although soil microbial communities and their impacts on plant communities have received extensive attention, comparatively little is known about leaf microbes and their interactions with plants and higher trophic levels, particularly in forests. We began a long-term research effort at the Barro Colorado Nature Monument in 2010 to assess the diversity, distribution, and impacts of foliar microbiomes – specifically bacteria that occur upon and within leaves –on seedlings and saplings of co-occurring tree species. We demonstrated that experimentally altering foliar microbiomes with commercial antibiotics had pervasive effects on plant traits, plant-plant interactions, and interactions with higher trophic levels. Taken together, our results suggest that these cryptic organisms may drive important trophic cascades and ecosystem-level patterns, including plant diversity, nutrient cycling, and net primary productivity in forest biomes.<p></p>

Zero-shot learning (ZSL) is to construct recognition models for unseen target classes that have no labeled samples for training. It utilizes the class attributes or semantic vectors as side information and transfers supervision information from related source classes with abundant labeled samples. Existing ZSL approaches adopt an intermediary embedding space to measure the similarity between a sample and the attributes of a target class to perform zero-shot classification. However, this way may suffer from the information loss caused by the embedding process and the similarity measure cannot fully make use of the data distribution. In this paper, we propose a novel approach which turns the ZSL problem into a conventional supervised learning problem by synthesizing samples for the unseen classes. Firstly, the probability distribution of an unseen class is estimated by using the knowledge from seen classes and the class attributes. Secondly, the samples are synthesized based on the distribution for the unseen class. Finally, we can train any supervised classifiers based on the synthesized samples. Extensive experiments on benchmarks demonstrate the superiority of the proposed approach to the state-of-the-art ZSL approaches.

Bioluminescence bacteria (BLB) are the most abundant and widely distributed light-emitting organisms that can be found in the marine environment. They are suitable for detecting pollution or integrated into bioluminescent imaging due to their ability to luminesce. However, there are limited studies regarding bioluminescent bacteria in terms of distribution and species present in Malaysia. This study aims to isolate BLB and amplify the luciferase (luxAB) genes. Bioluminescent bacteria were isolated from the guts of marine fish, Selaroidesleptolepis and streak onto luminescence agar (LA). The brightest luminous colony present in the dark was marked and streaked again obtain a pure colony. Then, the pure culture of the colony was subjected to genomic extraction before luxAB genes amplification and phylogenetic analysis. As a result, BLB were successfully isolated and identified to be Photobacteriumleiognathis train SYA2 (MZ491870.1). Genes encoding for luciferase enzyme were also amplified and sequenced with the size of luxA and luxB were 767 bp and 943 bp, respectively. Pairwise distance showed that the isolate has the highest similarity to P. leiognathi (DQ790853) with 99.66% and the lowest similarity to P. kishitanii (AY642227) with 69.84%. The information about the isolate will contribute to the distribution of BLB in Malaysia as well as potential of BLB as a biosensor and bioreporter.

Abstract. Structural damage identification is crucial for ensuring building safety, as it helps safeguard both lives and property. Recently, deep learning has become a prominent approach for damage detection. However, effective training of deep learning models requires abundant structural response data with accurate damage labels, which are often scarce in practical engineering applications. While existing models based on simulated data perform well in simulation environments, they typically struggle to achieve satisfactory performance on real-world measured data. To address this issue, this paper proposes a novel method for structural damage identification that combines transfer learning with the alignment of heterogeneous data (simulated and measured data). This method enables the transfer of damage detection capabilities from simulated data to measured data. First, finite element software is used to simulate various structural damage scenarios, generating a large volume of simulated data with precise damage labels. This data is then used to pre-train an initial model for damage identification. Next, transfer learning is applied, where the model is further trained using a combination of a small amount of measured data and the large simulated dataset. To address the distributional differences between the heterogeneous data sources, the Jensen-Shannon (JS) divergence is employed to quantify the discrepancy in the high-dimensional feature space. This is combined with the cross-entropy classification loss to form a composite loss function for model training. The resulting model is capable of accurately identifying structural damage in measured data. Experimental results show that this approach improves damage identification accuracy by 6% compared to traditional methods, demonstrating its effectiveness.

Problematic species, which include invasive, exotic, and harmful species, fragment native ecosystems, displace native plants and animals, and alter ecosystem function. In National Parks, such species negatively affect park resources and visitor enjoyment by altering landscapes and fire regimes, reducing native plant and animal habitat, and increasing trail maintenance needs. Recognizing these challenges, Heartland Inventory and Monitoring (I&M) Network parks identified problematic plants as the highest-ranking vital sign across the network. Given the need to provide early detection of potential problematic plants (ProPs) and the size of network parks, the Heartland I&M Network opted to allocate available sampling effort to maximize the area searched. With this approach and the available sampling effort in mind, we developed realistic objectives for the ProP monitoring protocol. The monitoring objectives are: 1. Create a watch list of ProPs known to occur in network parks and a watch list of potential ProPs that may invade network parks in the future, and occasionally update these two lists as new information is made available. 2. Provide early detection monitoring for all ProPs on the watch lists. 3. Search at least 0.75% and up to 40% of the reference frame for ProP occurrences in each park. 4. Estimate/calculate and report the abundance and frequency of ProPs in each park. 5. To the extent possible, identify temporal changes in the distribution and abundance of ProPs known to occur in network parks. ProP watch lists are developed using the best available and most relevant state, regional, and national exotic plant lists. The lists are generated using the PriorityDB database. We designed the park reference frames (i.e., the area to be monitored) to focus on accessible natural and restored areas. The field methods vary for small parks and large parks, defined as parks with reference frames less than and greater than 350 acres (142 ha), respectively. For small parks, surveyors make three equidistant passes through polygon search units that are approximately 2-acres (0.8 ha) in size. For large parks, surveyors record each ProP encountered along 200-m or 400-m line search units. The cover of each ProP taxa encountered in search units is estimated using the following cover scale: 0 = 0, 1 = 0.1-0.9 m2, 2 = 1-9.9 m2, 3 = 10-49.9 m2, 4 = 50-99.9 m2, 5 = 100-499.9 m2, 6 = 499.9-999.9 m2, and 7 = 1,000-4,999.9 m2. The field data are managed in the FieldDB database. Monitoring is scheduled to revisit most parks every four years. The network will report the results to park managers and superintendents after completing ProP monitoring.

Control of agro-associated pathogens is becoming increasingly difficult due to increased resistance and mounting restrictions on chemical pesticides and antibiotics. Likewise, in veterinary and human environments, there is increasing resistance of pathogens to currently available antibiotics requiring discovery of novel antibiotic compounds. These drawbacks necessitate discovery and application of microorganisms that can be used as biocontrol agents (BCAs) and the isolation of novel biologically-active compounds. This highly-synergistic one year project implemented an innovative pipeline aimed at detecting BCAs and associated biologically-active compounds, which included: (A) isolation of multidrug-resistant desert soil bacteria and root-associated bacteria from medicinal plants; (B) invitro screening of bacterial isolates against known plant, animal and human pathogens; (C) nextgeneration sequencing of isolates that displayed antagonistic activity against at least one of the model pathogens and (D) in-planta screening of promising BCAs in a model bean-Sclerotiumrolfsii system. The BCA genome data were examined for presence of: i) secondary metabolite encoding genes potentially linked to the anti-pathogenic activity of the isolates; and ii) rhizosphere competence-associated genes, associated with the capacity of microorganisms to successfully inhabit plant roots, and a prerequisite for the success of a soil amended BCA. Altogether, 56 phylogenetically-diverse isolates with bioactivity against bacterial, oomycete and fungal plant pathogens were identified. These strains were sent to Auburn University where bioassays against a panel of animal and human pathogens (including multi-drug resistant pathogenic strains such as A. baumannii 3806) were conducted. Nineteen isolates that showed substantial antagonistic activity against at least one of the screened pathogens were sequenced, assembled and subjected to bioinformatics analyses aimed at identifying secondary metabolite-encoding and rhizosphere competence-associated genes. The genome size of the bacteria ranged from 3.77 to 9.85 Mbp. All of the genomes were characterized by a plethora of secondary metabolite encoding genes including non-ribosomal peptide synthase, polyketidesynthases, lantipeptides, bacteriocins, terpenes and siderophores. While some of these genes were highly similar to documented genes, many were unique and therefore may encode for novel antagonistic compounds. Comparative genomic analysis of root-associated isolates with similar strains not isolated from root environments revealed genes encoding for several rhizospherecompetence- associated traits including urea utilization, chitin degradation, plant cell polymerdegradation, biofilm formation, mechanisms for iron, phosphorus and sulfur acquisition and antibiotic resistance. Our labs are currently writing a continuation of this feasibility study that proposes a unique pipeline for the detection of BCAs and biopesticides that can be used against phytopathogens. It will combine i) metabolomic screening of strains from our collection that contain unique secondary metabolite-encoding genes, in order to isolate novel antimicrobial compounds; ii) model plant-based experiments to assess the antagonistic capacities of selected BCAs toward selected phytopathogens; and iii) an innovative next-generation-sequencing based method to monitor the relative abundance and distribution of selected BCAs in field experiments in order to assess their persistence in natural agro-environments. We believe that this integrated approach will enable development of novel strains and compounds that can be used in large-scale operations.