A global model of the response of tropical and sub-tropical forest biodiversity to anthropogenic pressures

Habitat loss and degradation, driven largely by agricultural expansion and intensification, present the greatest immediate threat to biodiversity. Tropical forests harbour among the highest levels of terrestrial species diversity and are likely to experience rapid land-use change in the coming decades. Synthetic analyses of observed responses of species are useful for quantifying how land use affects biodiversity and for predicting outcomes under land-use scenarios. Previous applications of this approach have typically focused on individual taxonomic groups, analysing the average response of the whole community to changes in land use. Here, we incorporate quantitative remotely sensed data about habitats in, to our knowledge, the first worldwide synthetic analysis of how individual species in four major taxonomic groups—invertebrates, ‘herptiles’ (reptiles and amphibians), mammals and birds—respond to multiple human pressures in tropical and sub-tropical forests. We show significant independent impacts of land use, human vegetation offtake, forest cover and human population density on both occurrence and abundance of species, highlighting the value of analysing multiple explanatory variables simultaneously. Responses differ among the four groups considered, and—within birds and mammals—between habitat specialists and habitat generalists and between narrow-ranged and wide-ranged species.     

Focus: The Aging Brain: Neural stem/progenitor cells in Alzheimer’s disease

Alzheimer’s disease (AD) is the most prevalent neurodegenerative disease and a worldwide health challenge. Different therapeutic approaches are being developed to reverse or slow the loss of affected neurons. Another plausible therapeutic way that may complement the studies is to increase the survival of existing neurons by mobilizing the existing neural stem/progenitor cells (NSPCs) — i.e. “induce their plasticity” — to regenerate lost neurons despite the existing pathology and unfavorable environment. However, there is controversy about how NSPCs are affected by the unfavorable toxic environment during AD. In this review, we will discuss the use of stem cells in neurodegenerative diseases and in particular how NSPCs affect the AD pathology and how neurodegeneration affects NSPCs. In the end of this review, we will discuss how zebrafish as a useful model organism with extensive regenerative ability in the brain might help to address the molecular programs needed for NSPCs to respond to neurodegeneration by enhanced neurogenesis.     

Social network- and community-level influences on contraceptive use: evidence from rural Poland

The diffusion of ‘modern’ contraceptives—as a proxy for the spread of low-fertility norms—has long interested researchers wishing to understand global fertility decline. A fundamental question is how local cultural norms and other people''s behaviour influence the probability of contraceptive use, independent of women''s socioeconomic and life-history characteristics. However, few studies have combined data at individual, social network and community levels to simultaneously capture multiple levels of influence. Fewer still have tested if the same predictors matter for different contraceptive types. Here, we use new data from 22 high-fertility communities in Poland to compare predictors of the use of (i) any contraceptives—a proxy for the decision to control fertility—with those of (ii) ‘artificial’ contraceptives—a subset of more culturally taboo methods. We find that the contraceptive behaviour of friends and family is more influential than are women''s own characteristics and that community level characteristics additionally influence contraceptive use. Highly educated neighbours accelerate women''s contraceptive use overall, but not their artificial method use. Highly religious neighbours slow women''s artificial method use, but not their contraceptive use overall. Our results highlight different dimensions of sociocultural influence on contraceptive diffusion and suggest that these may be more influential than are individual characteristics. A comparative multilevel framework is needed to understand these dynamics.     

Human mobility patterns predict divergent epidemic dynamics among cities

The epidemic dynamics of infectious diseases vary among cities, but it is unclear how this is caused by patterns of infectious contact among individuals. Here, we ask whether systematic differences in human mobility patterns are sufficient to cause inter-city variation in epidemic dynamics for infectious diseases spread by casual contact between hosts. We analyse census data on the mobility patterns of every full-time worker in 48 Canadian cities, finding a power-law relationship between population size and the level of organization in mobility patterns, where in larger cities, a greater fraction of workers travel to work in a few focal locations. Similarly sized cities also vary in the level of organization in their mobility patterns, equivalent on average to the variation expected from a 2.64-fold change in population size. Systematic variation in mobility patterns is sufficient to cause significant differences among cities in infectious disease dynamics—even among cities of the same size—according to an individual-based model of airborne pathogen transmission parametrized with the mobility data. This suggests that differences among cities in host contact patterns are sufficient to drive differences in infectious disease dynamics and provides a framework for testing the effects of host mobility patterns in city-level disease data.     

Will Passive Protection Save Congo Forests?

Central Africa’s tropical forests are among the world’s largest carbon reserves. Historically, they have experienced low rates of deforestation. Pressures to clear land are increasing due to development of infrastructure and livelihoods, foreign investment in agriculture, and shifting land use management, particularly in the Democratic Republic of Congo (DRC). The DRC contains the greatest area of intact African forests. These store approximately 22 billion tons of carbon in aboveground live biomass, yet only 10% are protected. Can the status quo of passive protection — forest management that is low or nonexistent — ensure the preservation of this forest and its carbon? We have developed the SimCongo model to simulate changes in land cover and land use based on theorized policy scenarios from 2010 to 2050. Three scenarios were examined: the first (Historical Trends) assumes passive forest protection; the next (Conservation) posits active protection of forests and activation of the national REDD+ action plan, and the last (Agricultural Development) assumes increased agricultural activities in forested land with concomitant increased deforestation. SimCongo is a cellular automata model based on Bayesian statistical methods tailored for the DRC, built with the Dinamica-EGO platform. The model is parameterized and validated with deforestation observations from the past and runs the scenarios from 2010 through 2050 with a yearly time step. We estimate the Historical Trends trajectory will result in average emissions of 139 million t CO₂ year^-1 by the 2040s, a 15% increase over current emissions. The Conservation scenario would result in 58% less clearing than Historical Trends and would conserve carbon-dense forest and woodland savanna areas. The Agricultural Development scenario leads to emissions of 212 million t CO₂ year^-1 by the 2040s. These scenarios are heuristic examples of policy’s influence on forest conservation and carbon storage. Our results suggest that 1) passive protection of the DRC’s forest and woodland savanna is insufficient to reduce deforestation; and 2): enactment of a REDD+ plan or similar conservation measure is needed to actively protect Congo forests, their unique ecology, and their important role in the global carbon cycle.     

Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis

Recently, an extensive study of 2,748 polar bears (Ursus maritimus) from across their circumpolar range was published in PLOS ONE, which used microsatellites and mitochondrial haplotypes to apparently show altered population structure and a dramatic change in directional gene flow towards the Canadian Archipelago—an area believed to be a future refugium for polar bears as their southernmost habitats decline under climate change. Although this study represents a major international collaborative effort and promised to be a baseline for future genetics work, methodological shortcomings and errors of interpretation undermine some of the study’s main conclusions. Here, we present a reanalysis of this data in which we address some of these issues, including: (1) highly unbalanced sample sizes and large amounts of systematically missing data; (2) incorrect calculation of F_ST and of significance levels; (3) misleading estimates of recent gene flow resulting from non-convergence of the program BayesAss. In contrast to the original findings, in our reanalysis we find six genetic clusters of polar bears worldwide: the Hudson Bay Complex, the Western and Eastern Canadian Arctic Archipelago, the Western and Eastern Polar Basin, and—importantly—we reconfirm the presence of a unique and possibly endangered cluster of bears in Norwegian Bay near Canada’s expected last sea-ice refugium. Although polar bears’ abundance, distribution, and population structure will certainly be negatively affected by ongoing—and increasingly rapid—loss of Arctic sea ice, these genetic data provide no evidence of strong directional gene flow in response to recent climate change.     

Modeling the Pre-Industrial Roots of Modern Super-Exponential Population Growth

To Malthus, rapid human population growth—so evident in 18th Century Europe—was obviously unsustainable. In his Essay on the Principle of Population, Malthus cogently argued that environmental and socioeconomic constraints on population rise were inevitable. Yet, he penned his essay on the eve of the global census size reaching one billion, as nearly two centuries of super-exponential increase were taking off. Introducing a novel extension of J. E. Cohen''s hallmark coupled difference equation model of human population dynamics and carrying capacity, this article examines just how elastic population growth limits may be in response to demographic change. The revised model involves a simple formalization of how consumption costs influence carrying capacity elasticity over time. Recognizing that complex social resource-extraction networks support ongoing consumption-based investment in family formation and intergenerational resource transfers, it is important to consider how consumption has impacted the human environment and demography—especially as global population has become very large. Sensitivity analysis of the consumption-cost model''s fit to historical population estimates, modern census data, and 21^st Century demographic projections supports a critical conclusion. The recent population explosion was systemically determined by long-term, distinctly pre-industrial cultural evolution. It is suggested that modern globalizing transitions in technology, susceptibility to infectious disease, information flows and accumulation, and economic complexity were endogenous products of much earlier biocultural evolution of family formation''s embeddedness in larger, hierarchically self-organizing cultural systems, which could potentially support high population elasticity of carrying capacity. Modern super-exponential population growth cannot be considered separately from long-term change in the multi-scalar political economy that connects family formation and intergenerational resource transfers to wider institutions and social networks.     

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling

Understanding CRISPR-Cas systems—the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks—is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical ‘rich-get-richer’ mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.     

The Push and Pull of Land Use Policy: Reconstructing 150 Years of Development and Conservation Land Acquisition

The growth of human populations and their resource needs have stressed the conservation of natural land resources. Many policies and programs have been implemented to address the pressures on land resources and notwithstanding this pressure, significant acquisition of land for conservation has occurred throughout history in the U.S., and internationally. Here we assess the on-the-ground result of the evolution of land use policies in California as a pioneer forerunner, in the form of acquisition of land for conservation (i.e. Open Space), and its impact on the rest of the U.S. and beyond. To this end we describe the timeline and spatial representation of the growth of California’s conservation network over the last 150 years, and link it to the history of land use policies. We then assess whether conservation land acquisition has consistently grown through time or occurred in specific decades. About ¼ of the state is now designated Open Space. Fewer and larger areas conserved and acquired at the beginning of the 20^th century; the conservation network was complemented with a larger number of smaller sized properties. Despite acquisition of land in every decade, the process was uneven (E = 0.3 for California, E = 0.14±0.08 average for the state’s counties), mostly due to the large acquisitions and land set asides in the 1900s, followed by 1930s and 1940s. This process was a result of a comprehensive set of legislation that evolved through time, and resulted from the competing needs for development and conservation. Even with the impressive 174,000 km² of public lands in California, the future of California’s natural infrastructure and natural heritage cannot rely solely on these public lands, nor public agencies and their resources. Critically a future course of land preservation relying on the purchase of new lands – in California and beyond – for conservation is tremendously expensive.     

A World at Risk: Aggregating Development Trends to Forecast Global Habitat Conversion

A growing and more affluent human population is expected to increase the demand for resources and to accelerate habitat modification, but by how much and where remains unknown. Here we project and aggregate global spatial patterns of expected urban and agricultural expansion, conventional and unconventional oil and gas, coal, solar, wind, biofuels and mining development. Cumulatively, these threats place at risk 20% of the remaining global natural lands (19.68 million km²) and could result in half of the world’s biomes becoming >50% converted while doubling and tripling the extent of land converted in South America and Africa, respectively. Regionally, substantial shifts in land conversion could occur in Southern and Western South America, Central and Eastern Africa, and the Central Rocky Mountains of North America. With only 5% of the Earth’s at-risk natural lands under strict legal protection, estimating and proactively mitigating multi-sector development risk is critical for curtailing the further substantial loss of nature.