Wild Ungulate Decision-Making and the Role of Tiny Refuges in Human-Dominated Landscapes

Wildlife conservation in human-dominated landscapes requires that we understand how animals, when making habitat-use decisions, obtain diverse and dynamically occurring resources while avoiding risks, induced by both natural predators and anthropogenic threats. Little is known about the underlying processes that enable wild animals to persist in densely populated human-dominated landscapes, particularly in developing countries. In a complex, semi-arid, fragmented, human-dominated agricultural landscape, we analyzed the habitat-use of blackbuck, a large herbivore endemic to the Indian sub-continent. We hypothesized that blackbuck would show flexible habitat-use behaviour and be risk averse when resource quality in the landscape is high, and less sensitive to risk otherwise. Overall, blackbuck appeared to be strongly influenced by human activity and they offset risks by using small protected patches (~3 km²) when they could afford to do so. Blackbuck habitat use varied dynamically corresponding with seasonally-changing levels of resources and risks, with protected habitats registering maximum use. The findings show that human activities can strongly influence and perhaps limit ungulate habitat-use and behaviour, but spatial heterogeneity in risk, particularly the presence of refuges, can allow ungulates to persist in landscapes with high human and livestock densities.     

Contrasting Mode of Evolution at a Coat Color Locus in Wild and Domestic Pigs

Despite having only begun ~10,000 years ago, the process of domestication has resulted in a degree of phenotypic variation within individual species normally associated with much deeper evolutionary time scales. Though many variable traits found in domestic animals are the result of relatively recent human-mediated selection, uncertainty remains as to whether the modern ubiquity of long-standing variable traits such as coat color results from selection or drift, and whether the underlying alleles were present in the wild ancestor or appeared after domestication began. Here, through an investigation of sequence diversity at the porcine melanocortin receptor 1 (MC1R) locus, we provide evidence that wild and domestic pig (Sus scrofa) haplotypes from China and Europe are the result of strikingly different selection pressures, and that coat color variation is the result of intentional selection for alleles that appeared after the advent of domestication. Asian and European wild boar (evolutionarily distinct subspecies) differed only by synonymous substitutions, demonstrating that camouflage coat color is maintained by purifying selection. In domestic pigs, however, each of nine unique mutations altered the amino acid sequence thus generating coat color diversity. Most domestic MC1R alleles differed by more than one mutation from the wild-type, implying a long history of strong positive selection for coat color variants, during which time humans have cherry-picked rare mutations that would be quickly eliminated in wild contexts. This pattern demonstrates that coat color phenotypes result from direct human selection and not via a simple relaxation of natural selective pressures.     

Modern Hunting Practices and Wild Meat Trade in the Oil Palm Plantation-Dominated Landscapes of Sumatra,Indonesia

The ongoing expansion of plantation agriculture has changed the ecological, demographic, and social conditions of Southeast Asia’s forested areas, yet little is known about hunting practices in these novel landscapes. Using information from 73 in-depth interviews with hunters, agricultural workers and wild meat dealers in the Jambi province of Sumatra, Indonesia, we describe contemporary hunting practices, including how hunting methods, wildlife harvest and consumption rates vary between different indigenous and immigrant ethnic groups. Hunting is now primarily a commercial endeavor for harvesting wild boar (Sus scrofa) meat; over 7500 wild boars were sold in Jambi City alone in 2011. The Muslim majority avoids wild boar for religious reasons, but there is substantial local and export demand driven by Chinese and Christian Batak. We conclude that hunting within oil palm plantations may reduce crop damage from wild boar and also yield large amounts of wild meat with relatively little by-catch of threatened animals.     

Modeling and Mapping the Probability of Occurrence of Invasive Wild Pigs across the Contiguous United States

Wild pigs (Sus scrofa), also known as wild swine, feral pigs, or feral hogs, are one of the most widespread and successful invasive species around the world. Wild pigs have been linked to extensive and costly agricultural damage and present a serious threat to plant and animal communities due to their rooting behavior and omnivorous diet. We modeled the current distribution of wild pigs in the United States to better understand the physiological and ecological factors that may determine their invasive potential and to guide future study and eradication efforts. Using national-scale wild pig occurrence data reported between 1982 and 2012 by wildlife management professionals, we estimated the probability of wild pig occurrence across the United States using a logistic discrimination function and environmental covariates hypothesized to influence the distribution of the species. Our results suggest the distribution of wild pigs in the U.S. was most strongly limited by cold temperatures and availability of water, and that they were most likely to occur where potential home ranges had higher habitat heterogeneity, providing access to multiple key resources including water, forage, and cover. High probability of occurrence was also associated with frequent high temperatures, up to a high threshold. However, this pattern is driven by pigs’ historic distribution in warm climates of the southern U.S. Further study of pigs’ ability to persist in cold northern climates is needed to better understand whether low temperatures actually limit their distribution. Our model highlights areas at risk of invasion as those with habitat conditions similar to those found in pigs’ current range that are also near current populations. This study provides a macro-scale approach to generalist species distribution modeling that is applicable to other generalist and invasive species.     

Molecular Evolution in Static and Dynamical Landscapes

In an attempt to understand protein evolution, we address the issues ofhow much variety in the sequences is needed to prompt the evolution ofan enzyme from random polypeptides and how does cellular interactionaffect the dynamics of molecular evolution to allow genetic diversity inpopulation. The experimental evolution of phage-displayed randompolypeptides of about 140 amino acid residues panned with transition stateanalogue for an esterase reaction showed that even with a population sizeas small as ten, not only could significant varieties be found but also therandom polypeptides in each of the generation had great promise towardsdeveloping into functional proteins. Hence, it is evident that the enzymeevolution is prompted even within a small local area of the static landscapeof the sequence space. Considering that interaction among living cells is aninevitable event in natural evolution, its role was investigated through threeconsecutive rounds of random mutagenesis on the glutamine synthetasegene and chemostat culture of the transformed Escherichia colicellscontaining the mutated genes. The molecular phylogeny and populationdynamics show the coexistence of some mutants having different level ofglutamine synthetase at each generation. In addition, it was confirmed thatcellular interaction via the medium influences the stability of the coexistenceand bring forth fitness change to the coexisting members of the population,thereby, leading to a dynamical landscape. Based on experimental resultsreflecting the extent of interaction among members in population, here, Iproposed that protein evolution could change its mode from theoptimization on static landscape to diversification on dynamicallandscape.     

Hedgerows and Their Role in Agricultural Landscapes

Hedgerows, rows of trees or shrubs enclosing or separating fields, are man made. They are part of rural landscapes and should not be studied without considering the farming systems and the rural society as a whole. Their species composition depends on the history of the countryside, as well as current farming practices. Land use and boundary management play a major role in determining the floristic composition of hedgerows, and are strongly related to the grain size of the field's mosaic. Hedgerow networks, due to their rectilinear shape, and with their high degree of connection, enhance or interrupt many fluxes in the landscape. Hedgerows act as a corridor of movement and dispersal for many forest species, such as carabids, small mammals, and plants. On the other hand, hedgerows interrupt or slow down air fluxes and the propagules they carry. In the heterogeneous mosaic of fields and wooded patches, hedgerows often increase the functional connectivity of rural landscapes. The future of hedgerows depends on the changes of the rural society, which includes more and more nonfarmers. Hedgerows will be considered not only as a part of a productive area, but also as an element of a multifunctional landscape.     

Energy Landscapes and Catalysis in Nitric-oxide Synthase

Nitric oxide (NO) plays diverse roles in mammalian physiology. It is involved in blood pressure regulation, neurotransmission, and immune response, and is generated through complex electron transfer reactions catalyzed by NO synthases (NOS). In neuronal NOS (nNOS), protein domain dynamics and calmodulin binding are implicated in regulating electron flow from NADPH, through the FAD and FMN cofactors, to the heme oxygenase domain, the site of NO generation. Simple models based on crystal structures of nNOS reductase have invoked a role for large scale motions of the FMN-binding domain in shuttling electrons from the FAD-binding domain to the heme oxygenase domain. However, molecular level insight of the dynamic structural transitions in NOS enzymes during enzyme catalysis is lacking. We use pulsed electron-electron double resonance spectroscopy to derive inter-domain distance relationships in multiple conformational states of nNOS. These distance relationships are correlated with enzymatic activity through variable pressure kinetic studies of electron transfer and turnover. The binding of NADPH and calmodulin are shown to influence interdomain distance relationships as well as reaction chemistry. An important effect of calmodulin binding is to suppress adventitious electron transfer from nNOS to molecular oxygen and thereby preventing accumulation of reactive oxygen species. A complex landscape of conformations is required for nNOS catalysis beyond the simple models derived from static crystal structures of nNOS reductase. Detailed understanding of this landscape advances our understanding of nNOS catalysis/electron transfer, and could provide new opportunities for the discovery of small molecule inhibitors that bind at dynamic protein interfaces of this multidimensional energy landscape.     

Rewilding Abandoned Landscapes in Europe

For millennia, mankind has shaped landscapes, particularly through agriculture. In Europe, the age-old interaction between humans and ecosystems strongly influenced the cultural heritage. Yet European farmland is now being abandoned, especially in remote areas. The loss of the traditional agricultural landscapes and its consequences for biodiversity and ecosystem services is generating concerns in both the scientific community and the public. Here we ask to what extent farmland abandonment can be considered as an opportunity for rewilding ecosystems. We analyze the perceptions of traditional agriculture in Europe and their influence in land management policies. We argue that, contrary to the common perception, traditional agriculture practices were not environmentally friendly and that the standards of living of rural populations were low. We suggest that current policies to maintain extensive farming landscapes underestimate the human labor needed to sustain these landscapes and the recent and future dynamics of the socio-economic drivers behind abandonment. We examine the potential benefits for ecosystems and people from rewilding. We identify species that could benefit from land abandonment and forest regeneration and the ecosystem services that could be provided such as carbon sequestration and recreation. Finally, we discuss the challenges associated with rewilding, including the need to maintain open areas, the fire risks, and the conflicts between people and wildlife. Despite these challenges, we argue that rewilding should be recognized by policy-makers as one of the possible land management options in Europe, particularly on marginal areas.     

Osteochondrosis and Arthrosis in Pigs

Eight feeding experiments, each comprising 48 boars or gilts, were carried out. The factors feed level, Ca, P and protein levels were varied within practical physiological limits. The animals were slaughtered at close to 100 kg live weight. Lesions in joints and bones were of a noninfectious, non-rachitic nature and of the osteochondrosis and arthrosis type. Ten to 12 g Ca and approx. 10 g P/kg ration gave histomorphologically seemingly more optimum structure of the spongious bone tissue and a higher ash percentage in bones than 7 g Ca and 6 g P, or unbalanced mineral levels in the ration. However, there was no significant difference in degree or incidence of joint and bone lesions between mineral groups. Neither were there such differences present between feed level groups or protein level groups. This may for the feed level groups be partly due to the low feed level pigs having a longer period of time during which they were highly susceptible to the development of lesions. The low feed level animals had longer long bones at 100 kg live weight than the high feed level animals. The length of the vertebral column was, however, approximately similar in the 2 feed level groups. The angles of the condyles and head of the femur according to the length axis were influenced by feed level or growth rate, most probably by an effect on the endochondral ossification.     

Coexistence and Spread of Competitors in Heterogeneous Landscapes

Competition between species is ubiquitous in nature and therefore widely studied in ecology through experiment and theory. One of the central questions is under which conditions a (rare) invader can establish itself in a landscape dominated by a resident species at carrying capacity. Applying the same question with the roles of the invader and resident reversed leads to the principle that “mutual invasibility implies coexistence.” A related but different question is how fast a locally introduced invader spreads into a landscape (with or without competing resident), provided it can invade. We explore some aspects of these questions in a deterministic, spatially explicit model for two competing species with discrete non-overlapping generations in a patchy periodic environment. We obtain threshold values for fragmentation levels and dispersal distances that allow for mutual invasion and coexistence even if the non-spatial competition model predicts competitive exclusion. We obtain exact results when dispersal is governed by a Laplace kernel. Using the average dispersal success, we develop a mathematical framework to obtain approximate results that are independent of the exact dispersal patterns, and we show numerically that these approximations are very accurate.