A Blog Around The Clock

There are a bunch of new papers in PLoS Biology and PLoS Medicine and, somewhat out of usual schedule, in PLoS ONE. So, check out these and then look around for more:

Does Mutation Rate Depend on Itself:

Many a research paper, textbook chapter, and grant proposal has begun with the phrase “Mutation is the ultimate source of genetic variation.” Implicit in this phrase is the assumption that genetic variation is required for evolution. Without mutation, evolution would not be possible, and life itself could never have arisen in the first place. However, there is overwhelming evidence that the great majority of mutations with detectable effects are harmful [1-3]. Deleterious mutations are the price we living organisms pay for the ability to evolve.

Understanding the Web of Life: The Birds, the Bees, and Sex with Aliens:

When I was in school, I learned about a linear food chain in which, for example, flowers provide food for bees, which in turn are eaten by birds. The implications of this model are clear: if bees were to vanish, birds would starve and flowers would not be pollinated. Whether this concept was a hangover from the old idea of the great chain of being (scala naturæ) or a simplification deemed necessary for unsophisticated school children is unclear. Nevertheless, despite the appeal of this simple caricature, it couldn’t be further from the truth in most of the world’s ecosystems. Birds feed on a variety of plants and animals, and are themselves fed upon by mammals, other birds, a diverse array of parasites, and eventually carrion feeders. It takes little more than a passing glance at the natural world to notice that complexity is the rule, rather than the exception. Describing this complexity and understanding its importance, however, is anything but simple. Ecologists have for a long time struggled to find consistent patterns in the structure of complex webs of interacting species from disparate ecosystems. However, recent empirical and theoretical breakthroughs have begun to shed light on the structure of the web of life that connects living things, and the vulnerability of this web to perturbations such as the introduction of invasive alien species.

The Fall and Rise of US Inequities in Premature Mortality: 1960-2002:

Debates exist as to whether, as overall population health improves, the absolute and relative magnitude of income- and race/ethnicity-related health disparities necessarily increase–or derease. We accordingly decided to test the hypothesis that health inequities widen–or shrink–in a context of declining mortality rates, by examining annual US mortality data over a 42 year period. Using US county mortality data from 1960-2002 and county median family income data from the 1960-2000 decennial censuses, we analyzed the rates of premature mortality (deaths among persons under age 65) and infant death (deaths among persons under age 1) by quintiles of county median family income weighted by county population size. Between 1960 and 2002, as US premature mortality and infant death rates declined in all county income quintiles, socioeconomic and racial/ethnic inequities in premature mortality and infant death (both relative and absolute) shrank between 1966 and 1980, especially for US populations of color; thereafter, the relative health inequities widened and the absolute differences barely changed in magnitude. Had all persons experienced the same yearly age-specific premature mortality rates as the white population living in the highest income quintile, between 1960 and 2002, 14% of the white premature deaths and 30% of the premature deaths among populations of color would not have occurred. The observed trends refute arguments that health inequities inevitably widen–or shrink–as population health improves. Instead, the magnitude of health inequalities can fall or rise; it is our job to understand why.

The following three articles, two PLoS ONE research papers and a review in PLoS Biology are part of the same “package”, which, I hear, may be controversial in some circles (and I hope the expert bloggers will enlighten us all about it):

Shifting Baselines, Local Impacts, and Global Change on Coral Reefs:

Imagine trying to understand the ecology of tropical rainforests by studying environmental changes and interactions among the surviving plants and animals on a vast cattle ranch in the center of a deforested Amazon, without any basic data on how the forest worked before it was cleared and burned. The soil would be baked dry or eroded away and the amount of rainfall would be greatly decreased. Most of the fantastic biodiversity would be gone. The trees would be replaced by grasses or soybeans, the major grazers would be leaf-cutter ants and cattle, and the major predators would be insects, rodents, and hawks. Ecologists could do experiments on the importance of cattle for the maintenance of plant species diversity, but the results would be meaningless for understanding the rainforest that used to be or how to restore it in the future.

Fortunately, ecologists began to carefully describe tropical forests more than a century ago, and vast areas of largely intact forests have persisted until today, so there are meaningful baselines for comparison. Networks of 50-hectare plots are monitored around the world [1], and decades of experiments have helped to elucidate ecological mechanisms in these relatively pristine forests [2]. But the situation is very different for the oceans, because degradation of entire ecosystems has been more pervasive than on land [3] and underwater observations began much more recently. Monitoring of benthic ecosystems is commonly limited to small intertidal quadrats, and there is nothing like the high-resolution global monitoring network for tropical forests for any ocean ecosystem.

This lack of a baseline for pristine marine ecosystems is particularly acute for coral reefs, the so-called rainforests of the sea, which are the most diverse marine ecosystems and among the most threatened [4-8].

Baselines and Degradation of Coral Reefs in the Northern Line Islands:

Effective conservation requires rigorous baselines of pristine conditions to assess the impacts of human activities and to evaluate the efficacy of management. Most coral reefs are moderately to severely degraded by local human activities such as fishing and pollution as well as global change, hence it is difficult to separate local from global effects. To this end, we surveyed coral reefs on uninhabited atolls in the northern Line Islands to provide a baseline of reef community structure, and on increasingly populated atolls to document changes associated with human activities. We found that top predators and reef-building organisms dominated unpopulated Kingman and Palmyra, while small planktivorous fishes and fleshy algae dominated the populated atolls of Tabuaeran and Kiritimati. Sharks and other top predators overwhelmed the fish assemblages on Kingman and Palmyra so that the biomass pyramid was inverted (top-heavy). In contrast, the biomass pyramid at Tabuaeran and Kiritimati exhibited the typical bottom-heavy pattern. Reefs without people exhibited less coral disease and greater coral recruitment relative to more inhabited reefs. Thus, protection from overfishing and pollution appears to increase the resilience of reef ecosystems to the effects of global warming.

Microbial Ecology of Four Coral Atolls in the Northern Line Islands:

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (~5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world’s most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.