Towards a Molecular Taxonomy for Protists: Benefits,Risks, and Applications in Plankton Ecology

The increasing use of genetic information for the development of methods to study the diversity, distributions, and activities of protists in nature has spawned a new generation of powerful tools. For ecologists, one lure of these approaches lies in the potential for DNA sequences to provide the only immediately obvious means of normalizing the diverse criteria that presently exist for identifying and counting protists. A single, molecular taxonomy would allow studies of diversity across a broad range of species, as well as the detection and quantification of particular species of interest within complex, natural assemblages; goals that are not feasible using traditional methods. However, these advantages are not without their potential pitfalls and problems. Conflicts involving the species concept, disagreements over the true (physiological/ecological) meaning of genetic diversity, and a perceived threat by some that sequence information will displace knowledge regarding the morphologies, functions and physiologies of protistan taxa, have created debate and doubt regarding the efficacy and appropriateness of some genetic approaches. These concerns need continued discussion and eventual resolution as we move toward the irresistible attraction, and potentially enormous benefits, of the application of genetic approaches to protistan ecology.     

Pyrogeography,historical ecology,and the human dimensions of fire regimes

In our 2011 synthesis (Bowman et al., Journal of Biogeography, 2011, 38 , 2223–2236), we argued for a holistic approach to human issues in fire science that we term ‘pyrogeography’. Coughlan & Petty (Journal of Biogeography, 2013, 40 , 1010–1012) critiqued our paper on the grounds that our ‘pyric phase’ model was built on outdated views of cultural development, claiming we developed it to be the unifying explanatory framework for all human–fire sciences. Rather, they suggest that ‘historical ecology’ could provide such a framework. We used the ‘pyric transition’ for multiple purposes but did not offer it as an exclusive explanatory framework for pyrogeography. Although ‘historical ecology’ is one of many useful approaches to studying human–fire relationships, scholars should also look to political and evolutionary ecology, ecosystems and complexity theories, as well as empirical generalizations to build an interdisciplinary fire science that incorporates human, ecological and biophysical dimensions of fire regimes.     

Rewilding the Scottish Highlands: Do Wild Boar,Sus scrofa,Use a Suitable Foraging Strategy to be Effective Ecosystem Engineers?

Ecosystem engineers are increasingly being reintroduced to restore ecological processes in restoration and rewilding projects. To predict and adaptively manage the impact of such species their behavioral ecology must be understood and quantified. Rooting behavior by wild boar qualifies them as ecosystem engineers due to their impact on vegetation disturbance regimes. The behavioral foraging ecology of wild boar was quantified in a fenced area in the Scottish Highlands in order to provide some of the understanding necessary to predict their ability to affect ecosystem restoration. Five wild boar were monitored within a 125 ha fenced area using Global Positioning System (GPS) collars and behavioral monitoring over a 12‐month period. Their activity budget, the relationship between foraging behavior and vegetation communities, and how these relationships vary between seasons was investigated. The results indicate that wild boar invested approximately four more hours daily to rooting during the autumn and winter than the spring and summer. During the spring and summer, grazing was the dominant foraging behavior (approximately 28% of foraging period) while rooting dominated in autumn and winter (approximately 76% of foraging period). Deep rooting behavior is particularly associated with bracken‐dominated communities. Associations between rooting, vegetation community, and season will have a strong influence on the spatial and temporal distribution of rooting behavior. This variation could have important implications for the impacts of boar on vegetation community dynamics. These results detail some of wild boar's ecosystem engineering behaviors; however, further research is required to consider the wider impacts of a full reintroduction.     

The Philosophical Dullness of Classical Ecology, and a Levinsian Alternative

Ecology has had a lower profile in Biology & Philosophy than one might expect on the basis of the attention ecology is given in public discussions in relation to environmental issues. Our tentative explanation is that ecology appears theoretically redundant within biology and, consequently, philosophically challenging problemsrelated to biology are commonly supposed to be somewhere else, particularly in the molecular sphere. Richard Levins has recognized the genuine challenges posed by ecology for theoretical and philosophical thinking in biology. This essay sets the stage for appreciating his work; it was preceded by four articles published in Biology & Philosophy 15(2),and is followed by a personal reminiscent.     

Fairy rings,associated fungi,and assessment of their distribution across environmental variables using GIS

Fairy rings are conspicuous features of the Laramie Basin of southeastern Wyoming. Ten fairy ring sites chosen for intensive study were located using a small plane and 415 whole and partial fairy rings were georeferenced and ground-truthed. Fairy ring forming fungi were identified using a combination of taxonomy and ITS fungal barcode sequence comparisons. Precipitation, vegetation, soil type, elevation, slope, and slope aspect were queried using GIS. Eight fairy ring forming species were identified from the sites, including three unknown species, and two taxa not previously reported to form fairy rings. Most fairy rings occurred in drier mixed-grass prairie vegetation, whereas a small percentage occurred in mesic shrub dominated riparian vegetation. Most fungal species exhibited preferences for elevation and slope aspect, and rings were scarce on east facing slopes. The identity and autecology of individual fairy ring fungi and importance of environmental variables to fairy ring biology is discussed.     

Testosterone,physical activity,and somatic outcomes among Filipino males

Testosterone (T) facilitates male investment in reproduction in part through its anabolic effects on skeletal muscle. Traits like muscle and strength are energetically costly but are believed to enhance competitive ability in humans and other mammals. However, there are limited data on relationships between T and somatic outcomes in lean, non‐western populations. We evaluate relationships between waking and pre‐bed salivary T and adiposity, fat‐free mass (FFM), arm muscle area (AMA), and grip strength (GS) in a large, population‐based birth cohort of young adult Filipino males (20.8–22.6 years, n = 872). Data were collected as part of the Cebu Longitudinal Health and Nutrition Survey. Neither waking nor evening T predicted FFM, AMA, or GS. However, there were borderline or significant interactions between T and basketball playing (the most common team sport) and weight lifting as predictors of outcomes: higher waking T predicted higher FFM (activity × T interaction P < 0.01), AMA (interaction P < 0.1), and GS (interaction P < 0.02) among frequent basketball players, and GS (interaction P < 0.09) among the smaller sample of weight lifters. In contrast to clinical studies, but consistent with findings in several subsistence‐level populations, T was positively related to adiposity in these lean young males, suggesting that energy status might regulate circulating T. Our findings support a role of the prewaking rise in T as a determinant of energetic allocation to lean mass and strength in the context of repeated muscular use and support the hypothesized role of T as a mediator of investment in costly somatic traits in human males. Am J Phys Anthropol 142:590–599, 2010. © 2010 Wiley‐Liss, Inc.     

The medicinal leech, Hirudo medicinalis (L.) (Hirudinea: Gnathobdellae), at Dungeness, Kent

WILKIN, P. J., 1989. The medicinal leech, Hirudo medicinalis (L.) (Hirudinea: Gnathobdellae), at Dungeness, Kent . An account of the ecology and conservation of the medicinal leech ( Hirudo medicinalis (L.)) at Dungeness, Kent, is presented.     

BEMOVI,software for extracting behavior and morphology from videos,illustrated with analyses of microbes

Microbes are critical components of ecosystems and provide vital services (e.g., photosynthesis, decomposition, nutrient recycling). From the diverse roles microbes play in natural ecosystems, high levels of functional diversity result. Quantifying this diversity is challenging, because it is weakly associated with morphological differentiation. In addition, the small size of microbes hinders morphological and behavioral measurements at the individual level, as well as interactions between individuals. Advances in microbial community genetics and genomics, flow cytometry and digital analysis of still images are promising approaches. They miss out, however, on a very important aspect of populations and communities: the behavior of individuals. Video analysis complements these methods by providing in addition to abundance and trait measurements, detailed behavioral information, capturing dynamic processes such as movement, and hence has the potential to describe the interactions between individuals. We introduce BEMOVI, a package using the R and ImageJ software, to extract abundance, morphology, and movement data for tens to thousands of individuals in a video. Through a set of functions BEMOVI identifies individuals present in a video, reconstructs their movement trajectories through space and time, and merges this information into a single database. BEMOVI is a modular set of functions, which can be customized to allow for peculiarities of the videos to be analyzed, in terms of organisms features (e.g., morphology or movement) and how they can be distinguished from the background. We illustrate the validity and accuracy of the method with an example on experimental multispecies communities of aquatic protists. We show high correspondence between manual and automatic counts and illustrate how simultaneous time series of abundance, morphology, and behavior are obtained from BEMOVI. We further demonstrate how the trait data can be used with machine learning to automatically classify individuals into species and that information on movement behavior improves the predictive ability.     

Adult lake sturgeon (Acipenser fulvescens Rafinesque, 1817) occurrence in the Muskegon River system,a Lake Michigan drowned river mouth,USA

Recent advancements in telemetry have allowed managers and researchers to conduct comprehensive studies on the movement ecology of lake sturgeon (Acipenser fulvescens), a species of conservation concern in most of the Laurentian Great Lakes basin. In Michigan waters of Lake Michigan, drowned river mouth systems (a protected lake-like habitat that connects a river to lake) support 4 of 11 remaining lake sturgeon populations. One of those remnant populations is supported by the Muskegon River, a drowned river mouth system consisting of both Muskegon Lake and the Muskegon River. The objectives of this 6-year telemetry study were to determine whether adult lake sturgeon occupied the Muskegon River system outside of the spawning season (defined as March to July), to quantify their use of the system annually, and to identify and characterize patterns in occurrence. A total of 21 adult lake sturgeon implanted with acoustic transmitters were passively monitored throughout the year during 2012–2017. Eighty-two percent of tagged fish at large were detected ≥1 day in the Muskegon River system annually, and tagged lake sturgeon were frequently detected during both spawning and non-spawning time periods. Residency index (i.e., no. detection days/365 days) values indicated that adult lake sturgeon were not only detected throughout the year but that they occupied the Muskegon River system for an average of 130 days each year (residency index = 0.36 ± 0.05 SE) during our most spatially intensive acoustic monitoring in 2016–2017. Additionally, 24% of tagged lake sturgeon were primary residents (i.e., residency index >0.5) of the Muskegon River system in both years. Adult lake sturgeon followed 1 of 3 patterns of occurrence based on individual detection histories, and those patterns varied temporally and by the relative amount of use (i.e., high, medium, and low). Our findings build on previous research that found drowned river mouth systems in Lake Michigan can be important nursery habitats for juvenile lake sturgeon by showing that these habitats also can be used extensively by adult lake sturgeon throughout the year.     

四川南充市区火斑鸠的繁殖生态

20 0 2年 5～ 1 1月、2 0 0 3年 4～ 9月对南充市火斑鸠的繁殖生态进行了研究。结果表明 :4月下旬迁到 ,5月下旬开始繁殖 ;影响巢址选择的主要因素 6种 ;两性参与筑巢 ,营巢期 7～ 8d ;隔 2～ 3日产枚卵 ,窝卵数 ( 2 2 1± 0 0 9)枚 (n =1 9) ;雌雄轮流昼夜孵卵 ,日换孵两次 ,孵卵期 1 1～ 1 2d ,孵化率 92 86%;育雏可分三个时期 ,育雏高峰期每日 7:0 0、1 3 :0 0、1 8:0 0时左右 ,育雏期 1 7～ 1 8d ,雏离巢率 1 0 0 %,繁殖生产力1 86,种群育雏高峰期 7月和 8月上中旬 ;雏鸟于 1 7或 1 8日后离巢迁到郊外 ,9月下旬集群 ,1 0月中下旬迁飞。     

Freshwater ecology: changes, requirements, and future demands

The past development and evolution of limnology as a discipline has demonstrated that experimentally controlled disturbances of parts of aquatic ecosystems are essential for quantitative evaluation of causal mechanisms governing their operation. Correlative analyses and modeling only establish hypotheses, not causality, and allow only therapeutic management applications. Rather than constantly searching for differences, commonality must be sought. Among the large diversity of species, communities, and biogeochemical processes controlling growth and reproduction, commonality emerges at the levels of regulation of metabolism. Five areas of current and future limnological research are discussed in relation to greatest needs and promise to yield insights into material and energy flows in freshwater ecosystems and their effective management: (1) coupled metabolic mutualism in the physiological ecology of microbes (viruses, bacteria, fungi, and protists) and their biogeochemical, especially organic, couplings with the environment; (2) biochemical regulation of collective metabolism, recycling, and bioavailability of nutrients and growth regulators; (3) application of genetic and molecular techniques to addressing biogeochemical, evolutionary, and pollution remediation problems; (4) recognition that the metabolism within lakes and streams is dependent upon and regulated to a major extent by organic matter of the drainage basin and especially by the land-water interface biogeochemistry; and (5) recognition that food-web alterations ("biomanipulation") are short-term, expensive therapeutic tools that may minimize effects of eutrophication but will not solve or control eutrophication. Received: October 30, 1999 / Accepted: December 6, 1999     

Vegetation,fire and soil feedbacks of dynamic boundaries between rainforest,savanna and grassland

At fine spatial scales, savanna‐rainforest‐grassland boundary dynamics are thought to be mediated by the interplay between fire, vegetation and soil feedbacks. These processes were investigated by quantifying tree species composition, the light environment, quantities and flammability of fuels, bark thickness, and soil conditions across stable and dynamic rainforest boundaries that adjoin grassland and eucalypt savanna in the highlands of the Bunya Mountains, southeast Queensland, Australia. The size class distribution of savanna and rainforest stems was indicative of the encroachment of rainforest species into savanna and grassland. Increasing dominance of rainforest trees corresponds to an increase in woody canopy cover, the dominance of litter fuels (woody debris and leaf), and decline in grass occurrence. There is marked difference in litter and grass fuel flammability and this result is largely an influence of strongly dissimilar fuel bulk densities. Relative bark thickness, a measure of stem fire resistance, was found to be generally greater in savanna species when compared to that of rainforest species, with notable exceptions being the conifers Araucaria bidwillii and Araucaria cunninghamii. A transect study of soil nutrients across one dynamic rainforest – grassland boundary indicated the mass of carbon and nitrogen, but not phosphorus, increased across the successional gradient. Soil carbon turnover time is shortest in stable rainforest, intermediate in dynamic rainforest and longest in grassland highlighting nutrient cycling differentiation. We conclude that the general absence of fire in the Bunya Mountains, due to a divergence from traditional Aboriginal burning practices, has allowed for the encroachment of fire‐sensitive rainforest species into the flammable biomes of this landscape. Rainforest invasion is likely to have reduced fire risk via changes to fuel composition and microclimatic conditions, and this feedback will be reinforced by altered nutrient cycling. The mechanics of the feedbacks here identified are discussed in terms of landscape change theory.     

The Effects of Soil Type,Particle Size, Temperature,and Moisture on Reproduction of Belonolaimus longicaudatus

Effects of soil type, particle size, temperature, and moisture on the reproduction of Belonolaimus longicaudatus were investigated under greenhouse conditions. Nematode increases occurred only in soils with a minimum of 80% sand and a maximum of 10% clay. Optimum soil particle size for reproduction of the Tarboro, N.C. and Tifton, Ga. populations of the nematode was near that of 120-370 μm (65-mesh) silica sand. Reproduction was greatest at 25-30 C. Some reproduction by the Tifton, Ga. population occurred at 35 C, whereas the Tarboro, N.C. population declined, as compared to the initial inoculum. Both populations reproduced slightly at 20 C. Nematode reproduction was greater at a moisture level of 7% than at a high of 30% or a low of 2%. Reproduction occurred at the high moisture level only when the nutrient solution was aerated.     

Diet of Alouatta belzebul discolor in an Amazonian Rain Forest of Northern Mato Grosso State, Brazil

Prior field studies of Alouatta showed the highest frugivory in A. belzebul. During 10 mo between October 1999 and October 2000, we studied the feeding ecology of a group of 7–9 red-handed howlers (Alouatta belzebul discolor) in a primary forest on the banks of a tributary of the Teles Pires River, near Paranaíta, MT, Brazil (9°34S; 56°19W). The howlers used 3 types of habitat: upland (terra firme) forest, flood plain forest (igapó) and palm forest (açaizal). During 45 complete days of observation, the group fed on 67 plant species (N = 2039 feeding records) in 24 families. The 2 most used families were Leguminosae and Moraceae, with 17 species each. Fruits predominated (40–80%) in every month, except June, when young leaves accounted for 54% of the diet. Dialium guianense (Leguminosal, Caesalpinioideae) was the most consumed species. Flower (6%) and mature leaf (5%) consumptions were low. Tree bark, live and decayed wood, and woody twig monthly consumption varied from 0 to 26%, and occurred only in igapó, where they used mostly Macrolobium acaciaefolium (Leguminosae, Caesalpinioideae), Clitoria amazonum (Leguminosae, Papilionoideae) and Licania cf. canescens (Chrysobalanaceae). Our study on Alouatta belzebul discolor complements the high frugivory in A. b. belzebul and documents uncommon dietary items for the species. Although there is intraspecific variation in howler diets and new studies have shown higher frugivory for more folivorous species, Alouatta belzebul seems to be the most frugivorous howler species, in spite of its wide geographical distribution and, in this case, sympatry with Ateles chamek, a frugivore.     

A multivariate analysis integrating ecological,socioeconomic and physical characteristics to investigate urban forest cover and plant diversity in Beijing,China

Understanding the factors driving the variation in urban green space and plant communities in heterogeneous urban landscapes is crucial for maintaining biodiversity and important ecosystem services. In this study, we used a combination of field surveys, remote sensing, census data and spatial analysis to investigate the interrelationships among geographical and social-economic variables across 328 different urban structural units (USUs) and how they may influence the distributions of urban forest cover, plant diversity and abundance, within the central urban area of Beijing, China. We found that the urban green space coverage varied substantially across different types of USUs, with higher in agricultural lands (N = 15), parks (N = 46) and lowest in utility zones (N = 36). The amount of urban green space within USUs declines exponentially with the distance to urban center. Our study suggested that geographical, social and economic factors were closely related with each other in urban ecological systems, and have important impacts on urban forest coverage and abundance. The percentage of forest as well as high and low density urban areas were mainly responsible for variations in the data across all USUs and all land use/land cover types, and thus are important constituents and ecological indicators for understanding and modeling urban environment. Herb richness is more strongly correlated with tree and shrub density than with tree and shrub richness (r = −0.472, p < 0.05). However, other geographic and socioeconomic factors showed no significant relationships with urban plant diversity or abundance.     

Mark retention and fish survival associated with a low-cost marking technique for common carp Cyprinus carpio (Linnaeus, 1758)

Common carp (Cyprinus carpio, [Linnaeus, 1758]) have long been established in the United States and in some cases their populations can be very dense, leading biologists to expend significant effort towards reducing numbers of common carp in some populations. Estimating abundance of common carp prior to removal efforts would be useful in evaluating success of these removal efforts, but marking large numbers of fish can be expensive. Therefore, a low-cost tagging option is needed. In this study, we used tank and field experiments to determine the retention and longevity of hole-punch marks in the opercula of common carp. For the tank experiment, fish were double marked with a size-3 self-piercing tag and an operculum hole-punch mark (using a paper hole-punch tool with a hole diameter of 6.4 mm) on opposite sides of the fish. Over the entirety of the 180–day tank experiment, retention of the self-piercing tags and hole-punch marks was 100% and no marking mortality was observed. For the field experiment, 883 common carp were tagged at random in two groups, a double-marked group (n = 416, both self-piercing tags and hole-punch) and a single-mark group (n = 467, self-piercing tag). Fish were sampled monthly for 398 days. Because the length distribution sampled was bimodal, we evaluated tag retention of fish <330 mm TL (small fish, n = 273) and > 331 mm TL (large fish, n = 143), separately. Hole-punch mark retention was high for both size classes throughout most of the field experiment. For large fish, retention of hole-punch marks was 100% for the entire 398-day experiment. For small fish, retention of hole-punch marks was 100% through 184-day and remained above 93% through 328-days, but declined to 0% by day 398. Our results suggest that the operculum hole-punch mark is a valuable low-cost, long-term technique for tagging common carp.     

Autecology of the cryptic mysid crustacean,Heteromysis formosa S.I. Smith 1873, in a temperate estuary

The life history pattern, behavior, and distribution of the mysid crustacean,Heteromysis formosa, was studied in a temperate salt marsh. This mysid occurred in epibenthic sled collections every month, but was most abundant from June through November. Marsh creeks with irregular bottoms supported the largest populations, although some individuals occurred in other estuarine habitats and shallow ocean areas.Heteromysis formosa remains hidden on the bottom during the day and swims over open bottom at night. Many young fishes feed onH. formosa, especially at night. Seasonal changes in mysid abundance were related to the life history pattern. Reproduction was continuous from April through October. Overwintering populations of immature mysids were small. FemaleH. formosa were capable of reproducing more than one time. The number of young per brood ranged from 7 to 32 and was related to total adult body length.     

Zostera marina population genetics in Barnegat Bay, New Jersey, and implications for grass bed restoration

Within Barnegat Bay, New Jersey, Zostera marina populations have declined by 62% over the last 20 years, and restoration efforts have met with mixed success. We have completed a microsatellite-based genetic investigation of eight populations of Z. marina within Barnegat Bay to determine whether the genetic stock origins of the plants used in management projects may affect restoration success. Additionally, we assessed the genetic diversity of Z. marina in Barnegat Bay to better understand its population structure. Clonal diversity ranged from 0.70 to 0.95 for the populations studied. Individually, Barnegat Bay populations are not genetically diverse, and there is also little divergence among populations. The Atlantic populations had mean Hobs values (0.20–0.34) that were far lower than the Hexp values (0.69–0.83). Also, the F _IS values in all of the eastern populations indicate a surfeit of homozygotes over heterozygotes, suggesting a low degree of outcrossing in the Barnegat Bay populations. Six of the ten populations studied (Ham Island, Manahawkin Bay, Shelter Island, Marsh Elder, Harvey Cedar Sedge, and Long Island) show evidence of historical bottlenecks. Mean estimated F _ST values would suggest that most alleles are undergoing moderate genetic differentiation, with values that range from 0.06 to 0.13. Oyster Creek and Sedge Island demonstrate the largest estimated effective population sizes and may be the most appropriate populations for use in future eelgrass restoration projects.