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Scotch broom [Cytisus scoparius (L.) Link] is a large nonnative, leguminous shrub that threatens native plant communities by rapidly invading recently disturbed sites, competing vigorously for soil water and nutrients, and imparting soil legacy effects that inhibit native plants. In the Pacific Northwest, logging debris retention after forest harvesting prevents or slows C. scoparius invasions. A series of studies were conducted to determine potential mechanisms by which logging debris modifies the light environment to limit germination and growth of C. scoparius. In laboratory studies, seed germination did not vary significantly (P > 0.05): (1) between presence and absence of light for several temperature regimes, (2) when exposed to red (660 nm wavelength) versus far-red (730 nm wavelength) light, and (3) across a range of red/far-red light (R/FR) ratios. These results indicate that modification of the light environment by logging debris or plant canopies has little or no influence on C. scoparius germination. In a study to simulate effects of variable mass of logging debris, “heavy” debris (20000 kg ha-1) caused biologically relevant reductions in photosynthetic photon flux density (PPFD) and R/FR relative to conditions under “light” debris (10000 kg ha-1). Cytisus scoparius germination did not differ significantly between simulated heavy and light debris; however, values of seedling root and shoot biomass under heavy debris were 16% and 71% of those observed under light debris, respectively. These results indicate that heavy debris limits biomass of C. scoparius seedlings, particularly roots, by reducing both PPFD and R/FR, which increases seedling vulnerability to summer drought or other stressors. Retention of heavy logging debris after forest harvesting has potential application on sites likely to be invaded by C. scoparius, as well as those sites with seed banks containing C. scoparius.
The Drake equation has been used many times to estimate the number of observable civilizations in the galaxy. However, the uncertainty of the outcome is so great that any individual result is of limited use, as predictions can range from a handful of observable civilizations in the observable universe to tens of millions per Milky Way-sized galaxy. A statistical investigation shows that the Drake equation, despite its uncertainties, delivers robust predictions of the likelihood that the prevalent form of intelligence in the universe is artificial rather than biological. The likelihood of artificial intelligence far exceeds the likelihood of biological intelligence in all cases investigated. This conclusion is contingent upon a limited number of plausible assumptions. The significance of this outcome for the Fermi paradox is discussed.
The Developmental Origins of Health and Disease (DOHaD) states that intrauterine maternal environment influences postnatal life by programming offspring’s metabolism. Intrauterine milieu induced by exercise during pregnancy promotes long-lasting benefits to the offspring’s health and seems to offer some resistance against chronic diseases in adult life. Alzheimer’s disease is a public health concern with limited treatment options. In the present study, we assessed the potential of maternal exercise during pregnancy in long-term programming of young adult male rat offspring’s cerebellar metabolism in conferring neuroprotection against amyloid-β (Aβ) neurotoxicity. Female Wistar rats were submitted to a swimming protocol 1 week prior mating and throughout pregnancy (five sessions/a week lasting 30 min). Aβ oligomers were infused bilaterally in the brain ventricles of 60-day-old male offspring. Fourteen days after surgery, we measured parameters related to redox state, mitochondrial function, and the immunocontent of proteins related to synaptic function. We found that maternal exercise during pregnancy attenuated several parameters in the offspring’s male rat cerebellum, such as the reactive species rise, the increase of inducible nitric oxide synthase immunocontent and tau phosphorylation induced by Aβ oligomers, increased mitochondrial fission indicated by dynamin-related protein 1 (DRP1), and protein oxidation identified by carbonylation. Strikingly, we find that maternal exercise promotes changes in the rat offspring’s cerebellum that are still evident in young adult life. These favorable neurochemical changes in offspring’s cerebellum induced by maternal exercise may contribute to a protective phenotype against Aβ-induced neurotoxicity in young adult male rat offspring.
Giant reed (Arundo donax L.) recently was promoted as a biofuel crop in Oregon. Because giant reed is a highly invasive plant in North American rivers, the planting of this species in Oregon caused concern to scientists and local land managers. However, some growers in the area were interested in producing giant reed as a rotational crop. In order to find potential herbicides for weed control in giant reed or to control it as a volunteer, 13 foliar and 13 cut and spray herbicide treatments were pre-evaluated in greenhouse studies before conducting field trials. We chose 10% and 85% reduction in aboveground biomass for either crop safety or control, respectively. When applied at the standard rates, acetochlor and dimethenamid-p reduced aboveground dry biomass 10% or less. Acetochlor+atrazine, atrazine, flufenacet, and mesotrione reduced aboveground biomass at least 85% so have the potential for giant reed control.
Large carnivores have extensive spatial requirements, with ranges that often span geopolitical borders. Consequently, management of transboundary populations is subject to several political jurisdictions, often with heterogeneity in conservation challenges. In continental Asia there are four threatened leopard subspecies with transboundary populations spanning 23 countries: the Persian Panthera pardus saxicolor, Indochinese P. pardus delacouri, Arabian P. pardus nimr and Amur P. pardus orientalis leopards. We reviewed the status of these subspecies and examined the challenges to, and opportunities for, their conservation. The Amur and Indochinese leopards have the majority (58–100%) of their remaining range in borderlands, and the Persian and Arabian leopards have 23–26% of their remaining ranges in borderlands. Overall, in 18 of 23 countries the majority of the remaining leopard range is in borderlands, and thus in most countries conservation of these subspecies is dependent on transboundary collaboration. However, we found only two transboundary initiatives for Asian leopards. Overall, we highlighted three key transboundary landscapes in regions that are of high importance for the survival of these subspecies. Recent listing of the leopard in the Bonn Convention on the Conservation of Migratory Species of Wild Animals is important, but more international collaboration is needed to conserve these subspecies. We provide a spatial framework with which range countries and international agencies could establish transboundary cooperation for conserving threatened leopards in Asia.
This chapter introduces the statistical methods commonly applied by ecologists working with community data, by giving a general overview of the available tools. In this way, the chapter places joint species distribution models in general – and Hierarchical Modelling of Species Communities (HMSC) in particular – in the broader context of statistical community ecology. The chapter first introduces the wide variety of ordination methods and the substantial contributions they have made to empirical research in community ecology. The chapter next discusses the approaches of co-occurrence analysis and generalised linear models applied to diversity metrics. The chapter concludes by introducing species distribution modelling, highlighting the differences between single-species and joint species distribution models. Although the statistical methods are explained only verbally in this chapter, they are further discussed elsewhere in the book – namely, Chapters 4–8 give the statistical details on single-species and joint species distribution models, and Chapter 11 illustrates ordinations, co-occurrence analysis and joint species distribution models by applying them to a real data example.
This chapter discusses how Hierarchical Modelling of Species Communities (HMSC) can be used to model residual associations among species, with the aim of capturing biotic interactions. The chapter starts with an overview of the different modelling strategies that can be used for estimating biotic interactions in species distribution models. It then builds the statistical approach, first discussing the relationship between occurrence probabilities and co-occurrence probabilities and then describing how latent variables can be used to compactly model co-occurrences in species-rich communities. After introducing the baseline model, the chapter extends it to hierarchical, spatial and temporal study designs, as well as to cases where the biotic interactions depend on the environmental conditions. The chapter then focuses on interpretation, recalling that residual associations can be caused by many processes other than biotic interactions, therefore great caution must be taken when interpreting associations as biotic interactions. The chapter also discusses when and how the estimated species associations can be used to make improved predictions. The chapter finishes with two case studies, the first of which is based on simulated data and the second on sequencing data on dead-wood inhabiting fungi.
This chapter describes the types of data that empirical community ecologists typically collect, and how these can be incorporated in the Hierarchical Modelling of Species Communities (HMSC) framework as input. While community ecologists apply theoretical, experimental and observational approaches to studying the processes that structure ecological communities, this chapter (and the entire book) focuses mainly on empirical research based on non-manipulative observational data. Understanding the basic features of the data and how they have been collected will be essential for appropriately setting up the HMSC model and interpreting the results. The chapter describes each type of input HMSC data, namely the community data (i.e. the occurrences or abundances of the species), environmental data, data describing the spatio-temporal context, species trait data and phylogenetic data. Finally, the chapter discusses how to best organise the data, as well as how to solve problems arising from missing data.
This chapter moves to the area for which Hierarchical Modelling of Species Communities (HMSC) is really meant, namely multi-species modelling. Thus, the chapter moves from univariate generalised linear mixed models to multivariate generalised linear mixed models, where the response variable is the vector of species occurrences or abundances. The chapter starts by discussing the difference between stacked species distribution modelling and joint species distribution modelling. It then builds HMSC as a joint species distribution model, first discussing how to model variation among species niches in general, and then adding hierarchical levels to specifically model species niches as a function of species’ traits, phylogenetic relationships or a combination of the two. The chapter illustrates joint species distribution modelling by applying the R-package HMSC-R first to simulated data and then to real data on a plant community.
This chapter covers the basics of generalised linear mixed models in the univariate context of single-species distribution modelling. The chapter starts by discussing how species distribution models relate to the theory on environmental species niches. The modelling part of the chapter first introduces the linear model, then moves to generalised models, then to mixed models with both fixed and random effects, and finally describes how the explained variance can be partitioned among the explanatory variables. The applied part of the chapter uses both simulated and real data to illustrate how the R-package HMSC-R can be used to analyse generalised linear mixed models. While these analyses are rather standard and could also be conducted with many other packages, the reader is encouraged to go through them, as they provide the simplest way of becoming familiar with the syntax of HMSC-R.
Parakmeria omeiensis is a Critically Endangered tree species in the family Magnoliaceae, endemic to south-west China. The tree is functionally dioecious, but little is known about the species’ status in the wild. We investigated the range, population size, age structure, habitat characteristics and threats to P. omeiensis. We located a total of 74 individuals in two populations on the steep slopes of Mount Emei, Sichuan province, growing under the canopy of evergreen broadleaved forest in well-drained gravel soil. A male-biased sex ratio, lack of effective pollinating insects, and habitat destruction result in low seed set and poor seedling survival in the wild. We have adopted an integrated conservation approach, including strengthening in situ conservation, cultivation of saplings, ex situ conservation and reintroduction, to protect this species. The successful conservation of P. omeiensis has important implications for the conservation of the genus Parakmeria and the family Magnoliaceae.
Changed spatial configurations at sowing have been investigated as a strategy to minimize interspecific competition and improve the establishment and persistence of multi-species plantings in pastures, but the impact of this practice on the soil microbiome has received almost no previous research attention. Differences in populations of bacteria and fungi in the surface 10 cm of soil in the third year following pasture establishment were quantified using quantitative polymerase chain reaction and terminal restriction fragment length polymorphism methods. Populations were compared on, and between, drill rows sown to either the perennial grass phalaris (Phalaris aquatica L.), perennial legume lucerne (alfalfa; Medicago sativa L.) or the annual legume subterranean clover (Trifolium subterraneum L.). Results showed that soil microbial abundance and diversity were related to plant distribution across the field at the time of sampling and to soil chemical parameters including total carbon (C), mineral nitrogen (N), pH, and available phosphorus (P), potassium (K) and sulfur (S). Despite the 27-month lag since sowing, pasture species remained concentrated around the original drill row with very little colonization of the inter-row area. The abundance and diversity of bacterial and fungal populations were consistently greater under drill rows associated with higher total C concentrations in the surface soil compared with the inter-row areas. Our results showed that the pH and available nutrients were similar between the subterranean clover drill row and the inter-row, suggesting that soil microbial populations were not impacted directly by these soil fertility parameters, but rather were related to the presence or absence of plants. The abundance of bacteria and fungi were numerically lower under phalaris rows compared to rows sown to legumes. The richness and diversity of fungal populations were lowest between rows where lucerne was planted. Possible explanations for this observation include a lower C:N ratio of lucerne roots and/or a lack of fibrous roots at the soil surface compared to the other species, illustrating the influence of contrasting plant types on the soil microflora community. This study highlights the enduring legacy of the drill row on the spatial distribution of plants well into the pasture phase of a cropping rotation and discusses the opportunity to enhance the microbiome of cropping soils on a large scale during the pasture phase by increasing plant distribution across the landscape.
Plant breeding has brought about improvements in the herbage yield potential, forage quality and functional traits of perennial ryegrass (Lolium perenne L.). Under conditions of low external inputs, grassland swards based on perennial ryegrass often contain dicotyledonous species (legume and non-legume). Cultivar-specific functional traits such as growth form or phenology affect the competitive ability and yield in mixtures, but the extent to which cultivars with different functional traits affect forage quality in mixtures compared with pure stands is unknown. Therefore, we analysed four perennial ryegrass cultivars, each representing a combination of two functional traits with respect to phenology (early v. late heading) and growth form (upright v. prostrate) on forage quality, in a field experiment over 5 years. Each cultivar was grown in binary-mixtures with Trifolium repens L., as four-species mixtures with Taraxacum officinale L. and Plantago lanceolata L., and as grass monocultures. The effect of functional traits was dominant in the primary growth and persisted in pure stands but not in the mixtures from the third year onwards. Prostrate cultivars allowed the development of a greater proportion of clover and forbs within the mixtures, resulting in increased protein and energy and reduced fibre contents. In mixtures, forage quality was generally higher in the last regrowth. In conclusion, the indirect effects of growth form on forage quality due to modifications of botanical composition were more important than direct effects on forage quality.
The objective of the present study was to elucidate whether resveratrol could facilitate the survival of boar sperm during liquid preservation and fast cooling processes. Boar semen were diluted with Modena extender containing different concentrations of resveratrol. Sperm motility was evaluated by visual estimation. Membrane integrity, acrosome integrity and mitochondrial membrane potentials were measured by SYBR-14/PI, FITC-PNA and JC-1 staining, respectively. Moreover, the levels of reactive oxygen species (ROS), malonaldehyde (MDA) and total antioxidant capacity (T-AOC) were measured using commercial assay kits. B-cell lymphoma protein-2 (BCL2) content was determined by western blotting. During liquid preservation at 17oC, the addition of 50 μM resveratrol to the Modena extender significantly improved sperm motility, membrane integrity, acrosome integrity, and sperm mitochondrial membrane potentials. Similar results were also observed in the 150 μM resveratrol group during the fast cooling process. Furthermore, addition of resveratrol led to a decrease of ROS and MDA, and an increase in the content of T-AOC and BCL2. These observations suggest that addition of resveratrol to Modena extender protects boar sperm against oxidative stress. The optimal concentrations of resveratrol are 50 μM and 150 μM during liquid preservation and fast cooling process, respectively.
Wild poinsettia (Euphorbia heterophylla L.) is a troublesome broadleaf weed in grain production areas from South America. Herbicide resistance to multiple sites of action has been documented in this species, including protoporphyrinogen oxidase (PPO) inhibitors. We investigated the physiological and molecular bases for PPO resistance in a E. heterophylla population (R-PPO) from Southern Brazil. Whole-plant dose response experiments revealed a cross resistance profile to three different chemical groups of PPO inhibitors. Based on dose response parameters, R-PPO was resistant to lactofen (47.7-fold), saflufenacil (8.6-fold), and pyraflufen-ethyl (3.5-fold). Twenty-four h after lactofen treatment (120 g ha-1) in POST, R-PPO accumulated 27 times less protoporphyrin than the susceptible population (S-PPO). In addition, R-PPO generated 5 and 4.5 times less hydrogen peroxide and superoxide than S-PPO, respectively. The chloroplast PPO (PPO1) sequences were identical between the two populations, whereas 35 single nucleotide polymorphisms were found for the mitochondrial PPO (PPO2). Based on protein homology modeling, the R128L (homologous to R98L in common ragweed (Ambrosia artemisiifolia L.) was the only one located near the catalytic site, also in a conserved region of PPO2. The cytochrome P450 monooxygenase inhibitor malathion did not reverse resistance to lactofen in R-PPO, and both populations showed similar levels of PPO1 and PPO2 expression, suggesting that metabolic resistance and PPO overexpression are unlikely. This is the first report of a R128L mutation in PPO2 conferring cross resistance to PPO inhibitors in E. heterophylla.
The genus Megastigmus Dalman, 1820 (Hymenoptera: Megastigmidae) contains potential biocontrol agents of the invasive eucalypt galling chalcid Leptocybe spp. (Hymenoptera: Eulophidae), with several species reported in various parts of the world. Species discrimination is challenging due to intraspecific morphological variation, difficulty in measuring sizes of body parts, and the lack of information regarding the global distribution of parasitic Megastigmus. We used two species commonly associated with Leptocybe in its native range to review taxonomic methods and determine the most reliable morphological characters in species delimitation. We examined size variation of body characters, and conducted species discrimination using multivariate ratio analysis, mitochondrial Cytochrome c oxidase subunit 1 (COI) and nuclear 28S rDNA (28S) sequences. Morphological traits were effective in species delimitation yet revealed high variation in several characters employed in current keys. Knowledge generated on morphology and DNA justified the description of a new species, M. manonae, sp. n., the first record of M. pretorianensis in Australia, and revised diagnostic characters for M. zvimendeli. Based on these diagnostic characters and molecular data, we synonymize three species (M. judikingae, syn. n., from Australia, M. sichuanensis, syn. n., from China and M. icipeensis, syn. n., from Kenya) with M. zvimendeli. Our findings highlight the importance of molecular markers in assisting taxonomic decision-making and the need for coordinated work in identifying Megastigmus associated with Leptocybe spp.
Lysmata vittata is considered an invasive shrimp in the Atlantic Ocean and some characteristics might have contributed to its invasive success, such as its larval nutritional vulnerability during the early stages of development. The objective of this study was to evaluate the early larval stages of the shrimp L. vittata. Ovigerous specimens were captured in an estuarine region of north-eastern Brazil. Zoeae were assigned to two experiments: (1) the point of no return (PNR), consisting of treatments with an increasing number of days of starvation and subsequent days of feeding; and (2) the point of reserve saturation (PRS), consisting of treatments with an increasing number of days of feeding and subsequent days of starvation. Two control groups were considered: continuous starvation (CS) and continuous feeding (CF). Nutritional vulnerability was estimated by the time when 50% of the initially starved larvae (PNR50) lost the ability to moult to the next stage, when 50% of the initially fed larvae (PRS50) were capable of moulting to the next stage. In the CF, the mean development time (±SD) of the larvae that reached stage III was 4.36 ± 0.74 days with a mortality of 70%, and the mean carapace length (±SD) was 0.61 ± 0.04 mm CL. The PNR50 and PRS50 were 2.42 ± 0.14 and 1.32 ± 0.83 days, respectively. The nutritional vulnerability index (PRS50/PNR50 = 0.54) indicates that L. vittata presents intermediate dependence on exogenous food during the early larval stages, which might help our understanding of the invasive potential of this species in the Atlantic Ocean.
Overexploitation is a major threat to freshwater biodiversity. It chiefly affects vertebrates, mainly fishes, as well as reptiles, amphibians and a few mammals and birds, but some invertebrates are also subject to human depredation. Most capture is for food, but some species are taken for medicinal reasons, their skins, or for the aquarium trade. Overfishing became evident in Europe over 1000 years ago, when reductions in mean size and abundance of target species became evident. Size reduction in overexploited stocks is typical of non-fish also: this ‘great shrinking’ is a fingerprint of Anthropocene threats to biodiversity, reflecting both a reduction in the average size of individual species and in the mean body size of species making up assemblages. It results in ‘fishing down’ of food chains as smaller and smaller species are exploited in succession, and is evident in large rivers (Amazon, Yangtze, Ganges and Mekong), where it especially affects migratory species, and lakes (Malawi, Victoria). Statistics on freshwater capture yields are generally underestimates. Subsistence fishing contributes much to human welfare, but inadequate data limits fishery management options.
A considerable variety of Indonesian avifauna is forced into the domestic and international pet trade, where the majority of individuals are caught in the wild. To monitor the volume and development of the trade and to evaluate the threat status of the traded species, bird market surveys are usually performed. The most commonly used monitoring technique is the “Direct Counting Method – DCM”, i.e. the counting of openly displayed individuals offered for sale. In this study, we evaluate the reliability of the outputs that DCM delivers by conducting regular long-term bird censuses at two of the main animal markets in Medan (Sumatra, Indonesia) involving 10 major local vendors specialising in the Sumatran Laughingthrush (Garrulax bicolor; SL), our target species. Both markets were visited from March to December 2015 with three different survey intervals (one, two and four visits per month). In total, according to DCM, we recorded up to 461 SL individuals offered for sale. However, a comparison of the monthly logs recorded directly by the vendors during the same period revealed that DCM only uncovered a negligible proportion of the total trade. Specifically, we detected only 4.6%, 8.1% and 16.1% of the traded SL individuals in relation to the set survey intervals. While the numbers of recorded SL individuals according to DCM and the three survey intervals were significantly interrelated, none of them correlated with the real numbers of traded birds provided by the vendors. Our results suggest that census-based market data are underestimated, and represent an unknown proportion of true trade volumes, regardless of the intensity of visits. In order to obtain reliable data and prevent the underestimation of the volume of trade, we recommend of undisclosed monitoring of markets and the engagement of trusted individuals with a past personal interest in this field or, if possible, the vendors themselves.