Departures from neutrality induced by niche and relative fitness differences

Breaking the core assumption of ecological equivalence in Hubbell’s “neutral theory of biodiversity” requires a theory of species differences. In one framework for characterizing differences between competing species, non-neutral interactions are said to involve both niche differences, which promote stable coexistence, and relative fitness differences, which promote competitive exclusion. We include both in a stochastic community model in order to determine if relative fitness differences compensate for changes in community structure and dynamics induced by niche differences, possibly explaining neutral theory’s apparent success. We show that species abundance distributions are sensitive to both niche and relative fitness differences, but that certain combinations of differences result in abundance distributions that are indistinguishable from the neutral case. In contrast, the distribution of species’ lifetimes, or the time between speciation and extinction, differs under all combinations of niche and relative fitness differences. The results from our model experiment are inconsistent with the hypothesis of “emergent neutrality” and support instead a hypothesis that relative fitness differences counteract effects of niche differences on distributions of abundance. However, an even more developed theory of interspecific variation appears necessary to explain the diversity and structure of non-neutral communities.     

Speciation and the neutral theory of biodiversity

The neutral theory of biodiversity purports that patterns in the distribution and abundance of species do not depend on adaptive differences between species (i.e. niche differentiation) but solely on random fluctuations in population size (“ecological drift”), along with dispersal and speciation. In this framework, the ultimate driver of biodiversity is speciation. However, the original neutral theory made strongly simplifying assumptions about the mechanisms of speciation, which has led to some clearly unrealistic predictions. In response, several recent studies have combined neutral community models with more elaborate speciation models. These efforts have alleviated some of the problems of the earlier approaches, while confirming the general ability of neutral theory to predict empirical patterns of biodiversity. However, the models also show that the mode of speciation can have a strong impact on relative species abundances. Future work should compare these results to diversity patterns arising from non‐neutral modes of speciation, such as adaptive radiations.     

Footprints of ancient‐balanced polymorphisms in genetic variation data from closely related species

When long‐lasting, balancing selection can lead to “trans‐species” polymorphisms that are shared by two or more species identical by descent. In such cases, the gene genealogy at the selected site clusters by allele instead of by species, and nearby neutral sites also have unusual genealogies because of linkage. While this scenario is expected to leave discernible footprints in genetic variation data, the specific patterns remain poorly characterized. Motivated by recent findings in primates, we focus on the case of a biallelic polymorphism under ancient balancing selection and derive approximations for summaries of the polymorphism data from two species. Specifically, we characterize the length of the segment that carries most of the footprints, the expected number of shared neutral single nucleotide polymorphisms (SNPs), and the patterns of allelic associations among them. We confirm the accuracy of our approximations by coalescent simulations. We further show that for humans and chimpanzees—more generally, for pairs of species with low genetic diversity levels—these patterns are highly unlikely to be generated by neutral recurrent mutations. We discuss the implications for the design and interpretation of genome scans for ancient balanced polymorphisms in primates and other taxa.     

PREDICTING NUCLEAR GENE COALESCENCE FROM MITOCHONDRIAL DATA: THE THREE-TIMES RULE

Abstract.— Coalescence theory predicts when genetic drift at nuclear loci will result in fixation of sequence differences to produce monophyletic gene trees. However, the theory is difficult to apply to particular taxa because it hinges on genetically effective population size, which is generally unknown. Neutral theory also predicts that evolution of monophyly will be four times slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. Variation in mitochondrial DNA (mtDNA) within and between species has been studied extensively, but can these mtDNA data be used to predict coalescence in nuclear loci? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The “three‐times rule” states that, on average, most nuclear loci will be monophyletic when the branch length leading to the mtDNA sequences of a species is three times longer than the average mtDNA sequence diversity observed within that species. A test using mitochondrial and nuclear intron data from seven species of whales and dolphins suggests general agreement with predictions of the three‐times rule. We define the coalescence ratio as the mitochondrial branch length for a species divided by intraspecific mtDNA diversity. We show that species with high coalescence ratios show nuclear monophyly, whereas species with low ratios have polyphyletic nuclear gene trees. As expected, species with intermediate coalescence ratios show a variety of patterns. Especially at very high or low coalescence ratios, the three‐times rule predicts nuclear gene patterns that can help detect the action of selection. The three‐times rule may be useful as an empirical benchmark for evaluating evolutionary processes occurring at multiple loci.     

The SER Standards,cultural ecosystems,and the nature‐culture nexus—a reply to Evans and Davis

Evans and Davis claim the SER Standards use a “pure naturalness” model for restoration baselines and exclude most cultural ecosystems from the ecological restoration paradigm. The SER Standards do neither. The SER Standards consider both “natural” ecosystems (that are unequivocally not cultural) and “similar” cultural ecosystems as suitable reference models. Furthermore, Evans and Davis propose assessing whether a cultural ecosystem exhibits “good, bad, or neutral impacts from humans on ecosystems” as the basis for reference models. We argue that such an approach would overlook the indispensability of native ecosystem benchmarks to measure human impacts and provide a springboard for social‐ecological restoration.     

Neutrality at sea in transition: State practice in the gulf war as emerging international customary law∗

Abstract

This paper provides an appraisal of the continuing efficacy of the law of neutrality as it pertains to the balance of interests of belligerents and neutrals in the maritime environment. The author finds that international customary law of naval warfare pertaining to the rights of neutrals is emerging today as a result of State and extra‐State practice in the Gulf War. This is demonstrated by examination of belligerent and neutral conduct in the “Tanker War”; and various authoritative assessments of that conduct by the international community. The examination proceeds from an analysis of the underlying theory of the customary law‐making process and evolutionary nature of the law of neutrality since before World War II. State conduct in the Gulf War, including the employment of war‐exclusion zones, is critically examined against this backdrop. Discerned from this analysis are firm, “baseline”; standards of the law of neutrality against which State practice, belligerent as well as neutral, and ultimately the emerging customary law, may be assessed.     

THE COEVOLUTIONARY IMPLICATIONS OF HOST TOLERANCE

Host tolerance to infectious disease, whereby hosts do not directly “fight” parasites but instead ameliorate the damage caused, is an important defense mechanism in both plants and animals. Because tolerance to parasite virulence may lead to higher prevalence of disease in a population, evolutionary theory tells us that while the spread of resistance genes will result in negative frequency dependence and the potential for diversification, the evolution of tolerance is instead likely to result in fixation. However, our understanding of the broader implications of tolerance is limited by a lack of fully coevolutionary theory. Here we examine the coevolution of tolerance across a comprehensive range of classic coevolutionary host–parasite frameworks, including equivalents of gene‐for‐gene and matching allele and evolutionary invasion models. Our models show that the coevolution of host tolerance and parasite virulence does not lead to the generation and maintenance of diversity through either static polymorphisms or through “Red‐queen” cycles. Coevolution of tolerance may however lead to multiple stable states leading to sudden shifts in parasite impacts on host health. More broadly, we emphasize that tolerance may change host–parasite interactions from antagonistic to a form of “apparent commensalism,” but may also lead to the evolution of parasites that are highly virulent in nontolerant hosts.     

Colpodean ciliate phylogeny and reference alignments for phylogenetic placements

The Colpodea form a major clade of ciliates that are often found in environmental DNA sequencing studies. They are united by similar somatic ciliature, but differentiated by complex oral structures. Although there are four well supported colpodean subclades, there is disagreement in molecular phylogenetic inferences about their branching order. Using available nuclear SSU-rRNA sequences, we evaluated if the bursariomorphids or the platyophryids are sister to the remaining colpodeans. We inferred the “platyophryids-early” topologies using different alignment and masking methods, but constrained analyses could not reject the “bursariomorphids-early” topology. Both bursariomorphids and platyophryids clades have a similar number of nucleotide positions shared with the outgroup, and both are interconnected with the outgroup in phylogenetic networks. Based on these discordant results, it is hard to determine which clade branched off first, although the “platyophryids-early topology” is also supported by mitochondrial SSU-rRNA data. We also offer different reference alignments that can be used to phylogenetically place short- and long-read data from environmental DNA sequencing studies, and we propose some tentative evolutionary and ecological interpretations of those placements.     

Primary homologies of the circumorbital bones of snakes

Some snakes have two circumorbital ossifications that in the current literature are usually referred to as the postorbital and supraorbital. We review the arguments that have been proposed to justify this interpretation and provide counter‐arguments that reject those conjectures of primary homology based on the observation of 32 species of lizards and 81 species of snakes (both extant and fossil). We present similarity arguments, both topological and structural, for reinterpretation of the primary homologies of the dorsal and posterior orbital ossifications of snakes. Applying the test of similarity, we conclude that the posterior orbital ossification of snakes is topologically consistent as the homolog of the lacertilian jugal, and that the dorsal orbital ossification present in some snakes (e.g., pythons, Loxocemus, and Calabaria) is the homolog of the lacertilian postfrontal. We therefore propose that the terms postorbital and supraorbital should be abandoned as reference language for the circumorbital bones of snakes, and be replaced with the terms jugal and postfrontal, respectively. The primary homology claim for the snake “postorbital” fails the test of similarity, while the term “supraorbital” is an unnecessary and inaccurate application of the concept of a neomorphic ossification, for an element that passes the test of similarity as a postfrontal. This reinterpretation of the circumorbital bones of snakes is bound to have important repercussions for future phylogenetic analyses and consequently for our understanding of the origin and evolution of snakes. J. Morphol. 274:973–986, 2013. © 2013 Wiley Periodicals, Inc.     

Oddity,predation risk and social decisions in aquatic invertebrates

Group living is widespread across animal taxa, incurring benefits such as increased foraging efficiency or an enhanced chance of surviving a predator's attack. The chances of escaping a predator are often lower for odd‐looking individuals, as these are detected at a higher rate than uniform looking group members. While this “oddity effect” shall operate in animals differing in any given phenotype, including colour, size or species identity, it has been experimentally tested mainly for odd‐coloured individuals. We examined the oddity effect and swarming preferences in two differently sized species of freshwater planktonic crustaceans (large Daphnia magna and small Daphnia pulex). We experimentally investigated whether odd individuals in a swarm of heterospecific Daphnia were more vulnerable to predation by a common predator, the three‐spined stickleback (Gasterosteus aculeatus). Furthermore, Daphnia's swarming preference was tested by giving individuals the opportunity to choose between conspecific/heterospecific odour and a neutral control. In contrast to the predictions of the oddity effect, odd individuals were not always preyed on earlier; instead three‐spined stickleback preferentially predated large, more nutritious individuals. Daphnia of both species reacted towards the perception of con‐ and heterospecifics odours. While D. pulex generally avoided the smell of other daphnids, D. magna avoided conspecifics but tended to prefer heterospecifics over the neutral control. These findings provide new insights into swarming strategies and social preference of an invertebrate and how this behaviour can influence predation risk.     

A novel genealogical approach to neutral biodiversity theory

Current neutral theory in community ecology views local biodiversity as a result of the interplay between speciation, extinction and immigration. Simulations and a mean‐field approximation have been used to study this neutral theory. As simulations have limitations of convergence and the mean‐field approximation ignores dependencies between species’ abundances when applied to species‐abundance data, there is still no final conclusion whether the neutral theory or the traditional lognormal model describes community structure best. We present a novel analytical framework, based on the genealogy of individuals in the local community, to overcome the problems of previous approaches, and show, using Bayesian statistics, that the lognormal model provides a slightly better fit to the species‐abundance distribution of a much‐discussed tropical tree community. A key feature of our approach is that it shows the tight link between genetic and species diversity, which creates important perspectives to future integration of evolutionary and community ecological theory.     

Autoimmunity and the microbiome: T‐cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts

I propose a T‐cell receptor (TcR)‐based mechanism by which immunity mediates both “genetic self” and “microbial self” thereby, connecting microbiome disease with autoimmunity. The hypothesis is based on simple principles. First, TcR are selected to avoid strong cross‐reactivity with “self,” resulting in selection for a TcR repertoire mimicking “genetic self.” Second, evolution has selected for a “microbial self” that mimics “genetic self” so as to share tolerance. In consequence, our TcR repertoire also mimics microbiome antigenicity, providing a novel mechanism for modulating tolerance to it. Also, the microbiome mimics the TcR repertoire, acting as a secondary immune system. I call this TcR‐microbiome mimicry “holoimmunity” to denote immune tolerance to the “holobiont self.” Logically, microbiome‐host mimicry means that autoimmunity directed at host antigens will also attack components of the microbiome, and conversely, an immunological attack on the microbiome may cross‐react with host antigens producing “holoautoimmunity.”

     

Harmonia axyridis invasions: Deducing evolutionary causes and consequences

I consider evolutionary approaches to deducing factors that have made the ladybird beetle Harmonia axyridis such a successful invader, and the contribution that studies of this species in its native range can make. Work aiming to demonstrate which (pre)adaptations have made the species so successful often fails to compare these putative characters with those of other ladybirds. This has led to a tendency for “argument by design”‐type claims on characters widely shared by non‐invasive coccinellids. There is good evidence from genetic studies that evolutionary change occurred in invasive populations, contributing to their success. There is some evidence for subsequent evolutionary change after the establishment of invasive H. axyridis, primarily in the native organisms with which the ladybird interacts. I show here that there appears to have been little adaptation in H. axyridis, over about 20 generations, to the alkaloids of one North American native intraguild prey, the ladybird Coleomegilla maculata. Studies of H. axyridis in its native range are important, as they provide a snapshot of the ancestral ladybird, unobscured by subsequent evolutionary change related to its invasiveness. They provide baseline data about phenomena such as interactions with natural enemies and intraguild predation, and they also can provide pointers as to how H. axyridis might further adapt in the regions it has colonized. Harmonia axyridis represents an ideal opportunity for greater international co‐operation between scientists studying this species in its native range in Asia and scientists studying it in Europe, America and Africa, where it is an invasive exotic.     

The cultural construction of gendered bodies: Biology and metaphors of production and destruction*

One way of conceiving of the anthropological task is that of countering the degradations and “dehumanizations” of the “other” to which the species is prone by promoting “transcendent humanization.” However efficiently and professionally anthropologists gather their materials and form them into their ethnographic and ethnologic analyses, may not this “ethical impulse” be postulated as the “final cause” of our efforts? But what could such a sonorous phrase mean ? And what is its relationship to the systematic study of the “differences that make or do not make a difference” in culture to which anthropology has long been devoted? I will argue that it involves a dynamic of categories and that this dynamic is itself an object of systematic study. Recently, for example, some anthropologists have been writing “against culture,” seeing the culture concept and associated theory more as barriers than as benefits to pan‐human understanding. I will argue that this is an instance of “transcendent humanization.” One cannot but be sympathetic to the thrust and merits of this argument. But at the same time one wants to ask what implications it holds for the systematic study and understanding of the other. This article, then, examines some elementary vectors in the “dynamic of the categorical” involved in these and related recent debates which also may be seen in terms of transcendence and humanization: the debate over relativism and the recently emergent debate over “enlightenment mythmaking” in anthropology.     

Partial protection from cyclical selection generates a high level of polymorphism at multiple non‐neutral sites

Temporally varying selection is known to maintain genetic polymorphism under certain restricted conditions. However, if part of a population can escape from selective pressure, a condition called the “storage effect” is produced, which greatly promotes balanced polymorphism. We investigate whether seasonally fluctuating selection can maintain polymorphism at multiple loci, if cyclically fluctuating selection is not acting on a subpopulation called a “refuge.” A phenotype with a seasonally oscillating optimum is determined by alleles at multiple sites, across which the effects of mutations on phenotype are distributed randomly. This model resulted in long‐term polymorphism at multiple sites, during which allele frequencies oscillate heavily, greatly increasing the level of nonneutral polymorphism. The level of polymorphism at linked neutral sites was either higher or lower than expected for unlinked neutral loci. Overall, these results suggest that for a protein‐coding sequence, the nonsynonymous‐to‐synonymous ratio of polymorphism may exceed one. In addition, under randomly perturbed environmental oscillation, different sets of sites may take turns harboring long‐term polymorphism, thus making trans‐species polymorphism (which has been predicted as a classical signature of balancing selection) less likely.     

Organismal Aging and Oxidants beyond Macromolecules Damage

The relationship between oxidants and organismal aging was first articulated through the free radical theory of aging. One of the major predictions of the free radical theory of aging is that oxidative stress shortens organisms’ lifespan because of an increased level of oxidants, which are damaging to macromolecules. However, challenging the role of oxidants in age‐related diseases, there is now sufficient evidence that antioxidant supplements do not provide significant health benefits. Interestingly, in addition to an increase in oxidant‐mediated macromolecules damage, there is convincing experimental data to support the role of senescent cells in the process of aging. Here, the current knowledge regarding the role of oxidants and cellular senescence in organismal aging is reviewed and it is proposed that, in addition to the role of oxidants as inducers of macromolecular damage, oxidants may also function as regulators of signaling pathways involved in the establishment of cellular senescence. If this role for oxidants is established, it may be necessary to modify the free radical theory of aging from “Organisms age because cells accumulate reactive oxygen species‐dependent damage over time” to: “Organisms age because cells accumulate oxidants’‐dependent damage and oxidants’‐dependent senescent characteristics over time.”     

An “orientation sphere” visualization for examining animal head movements

1. Animal behavior is elicited, in part, in response to external conditions, but understanding how animals perceive the environment and make the decisions that bring about these behavioral responses is challenging.
2. Animal heads often move during specific behaviors and, additionally, typically have sensory systems (notably vision, smell, and hearing) sampling in defined arcs (normally to the front of their heads). As such, head‐mounted electronic sensors consisting of accelerometers and magnetometers, which can be used to determine the movement and directionality of animal heads (where head “movement” is defined here as changes in heading [azimuth] and/or pitch [elevation angle]), can potentially provide information both on behaviors in general and also clarify which parts of the environment the animals might be prioritizing (“environmental framing”).
3. We propose a new approach to visualize the data of such head‐mounted tags that combines the instantaneous outputs of head heading and pitch in a single intuitive spherical plot. This sphere has magnetic heading denoted by “longitude” position and head pitch by “latitude” on this “orientation sphere” (O‐sphere).
4. We construct the O‐sphere for the head rotations of a number of vertebrates with contrasting body shape and ecology (oryx, sheep, tortoises, and turtles), illustrating various behaviors, including foraging, walking, and environmental scanning. We also propose correcting head orientations for body orientations to highlight specific heading‐independent head rotation, and propose the derivation of O‐sphere‐metrics, such as angular speed across the sphere. This should help identify the functions of various head behaviors.
5. Visualizations of the O‐sphere provide an intuitive representation of animal behavior manifest via head orientation and rotation. This has ramifications for quantifying and understanding behaviors ranging from navigation through vigilance to feeding and, when used in tandem with body movement, should provide an important link between perception of the environment and response to it in free‐ranging animals.

     

Secondary osteon size and collagen/lamellar organization (“osteon morphotypes”) are not coupled,but potentially adapt independently for local strain mode or magnitude

In bone, matrix slippage that occurs at cement lines of secondary osteons during loading is an important toughening mechanism. Toughness can also be enhanced by modifications in osteon cross-sectional size (diameter) for specific load environments; for example, smaller osteons in more highly strained “compression” regions vs. larger osteons in less strained “tension” regions. Additional osteon characteristics that enhance toughness are distinctive variations in collagen/lamellar organization (i.e., “osteon morphotypes”). Interactions might exist between osteon diameter and morphotype that represent adaptations for resisting deleterious shear stresses that occur at the cement line. This may be why osteons often have a peripheral ring (or “hoop”) of highly oblique/transverse collagen. We hypothesized that well developed/distinct “hoops” are compensatory adaptations in cases where increased osteon diameter is mechanically advantageous (e.g., larger osteons in “tension” regions would have well developed/distinct “hoops” in order to resist deleterious consequences of co-existing localized shear stresses). We tested this hypothesis by determining if there are correlations between osteon diameters and strongly hooped morphotypes in “tension”, “compression”, and “neutral axis” regions of femora (chimpanzees, humans), radii (horse, sheep) and calcanei (horse, deer). The results reject the hypothesis—larger osteons are not associated with well developed/distinct “hoops”, even in “tension regions” where the effect was expected to be obvious. Although osteon diameter and morphotype are not coupled, osteon diameters seem to be associated with increased strain magnitudes in some cases, but this is inconsistent. By contrast, osteon morphotypes are more strongly correlated with the distribution of tension and compression.