EMMLi: A maximum likelihood approach to the analysis of modularity

Identification of phenotypic modules, semiautonomous sets of highly correlated traits, can be accomplished through exploratory (e.g., cluster analysis) or confirmatory approaches (e.g., RV coefficient analysis). Although statistically more robust, confirmatory approaches are generally unable to compare across different model structures. For example, RV coefficient analysis finds support for both two‐ and six‐module models for the therian mammalian skull. Here, we present a maximum likelihood approach that takes into account model parameterization. We compare model log‐likelihoods of trait correlation matrices using the finite‐sample corrected Akaike Information Criterion, allowing for comparison of hypotheses across different model structures. Simulations varying model complexity and within‐ and between‐module contrast demonstrate that this method correctly identifies model structure and parameters across a wide range of conditions. We further analyzed a dataset of 3‐D data, consisting of 61 landmarks from 181 macaque (Macaca fuscata) skulls, distributed among five age categories, testing 31 models, including no modularity among the landmarks and various partitions of two, three, six, and eight modules. Our results clearly support a complex six‐module model, with separate within‐ and intermodule correlations. Furthermore, this model was selected for all five age categories, demonstrating that this complex pattern of integration in the macaque skull appears early and is highly conserved throughout postnatal ontogeny. Subsampling analyses demonstrate that this method is robust to relatively low sample sizes, as is commonly encountered in rare or extinct taxa. This new approach allows for the direct comparison of models with different parameterizations, providing an important tool for the analysis of modularity across diverse systems.     

A COMPARISON OF COVARIANCE STRUCTURE IN WILD AND LABORATORY MUROID CRANIA

Mutations have the ability to produce dramatic changes to covariance structure by altering the variance of covariance-generating developmental processes. Several evolutionary mechanisms exist that may be acting interdependently to stabilize covariance structure, despite this developmental potential for variation within species. We explore covariance structure in the crania of laboratory mouse mutants exhibiting mild-to-significant developmental perturbations of the cranium, and contrast it with covariance structure in related wild muroid taxa. Phenotypic covariance structure is conserved among wild muroidea, but highly variable and mutation-dependent within the laboratory group. We show that covariance structures in natural populations of related species occupy a more restricted portion of covariance structure space than do the covariance structures resulting from single mutations of significant effect or the almost nonexistent genetic differences that separate inbred mouse strains. Our results suggest that developmental constraint is not the primary mechanism acting to stabilize covariance structure, and imply a more important role for other mechanisms.     

The AAT1 locus is critical for the biosynthesis of esters contributing to ‘ripe apple’ flavour in ‘Royal Gala’ and ‘Granny Smith’ apples

The ‘fruity’ attributes of ripe apples (Malus × domestica) arise from our perception of a combination of volatile ester compounds. Phenotypic variability in ester production was investigated using a segregating population from a ‘Royal Gala’ (RG; high ester production) × ‘Granny Smith’ (GS; low ester production) cross, as well as in transgenic RG plants in which expression of the alcohol acyl transferase 1 (AAT1) gene was reduced. In the RG × GS population, 46 quantitative trait loci (QTLs) for the production of esters and alcohols were identified on 15 linkage groups (LGs). The major QTL for 35 individual compounds was positioned on LG2 and co‐located with AAT1. Multiple AAT1 gene variants were identified in RG and GS, but only two (AAT1‐RGa and AAT1‐GSa) were functional. AAT1‐RGa and AAT1‐GSa were both highly expressed in the cortex and skin of ripe fruit, but AAT1 protein was observed mainly in the skin. Transgenic RG specifically reduced in AAT1 expression showed reduced levels of most key esters in ripe fruit. Differences in the ripe fruit aroma could be perceived by sensory analysis. The transgenic lines also showed altered ratios of biosynthetic precursor alcohols and aldehydes, and expression of a number of ester biosynthetic genes increased, presumably in response to the increased substrate pool. These results indicate that the AAT1 locus is critical for the biosynthesis of esters contributing to a ‘ripe apple’ flavour.     

‘I am helping them’: ‘Traffickers’, ‘anti‐traffickers’ and economies of bad faith

For several years, aid programs in the Mekong region have taken an increasing interest in cross‐border mobility and human trafficking and its relationship with development. More recently, there has been an increasing interest in the identification of trafficked victims and the investigation, arrest and prosecution of traffickers. Whereas anti‐trafficking programs ubiquitously define themselves as being in a battle with traffickers, this article argues that although they are not homologous social actors, both engage in acts of bad faith. The article elaborates this argument by drawing attention to the recruitment process within the Lao sex industry as well as to the way in which aid programs attempt to identify trafficked victims. It concludes that imaginary aspects of development underpin a simultaneous disjuncture yet enable the social reproduction of the life worlds of ‘traffickers’ and ‘anti‐traffickers’ alike.     

Linking ‘10‐year’ herbivore cycles to the lunisolar oscillation: the cosmic ray hypothesis

The mean population cycle periods of the snowshoe hare Lepus americanus, the larch budmoth Zeiraphera diniana, and the autumnal moth Epirrita autumnata are 9.3 years, similar to the lunar nodal phase cycle. When the full/new Moon is situated close to the ecliptic plane at solstice, it interacts more strongly with the magnetosphere, which plays a crucial role in protecting the Earth against ionizing cosmic ray particles. Ionization by cosmic rays induces protein mobilization in plants, which may increase forage quality for herbivores. Series of hare/lynx population indices from Canadian provinces and an autumnal moth series from Fennoscandia correlated with the lunar nodal phase cycle with different time lags. Both the time lag and the impact of an active sun, which increases solar energetic particles, but decreases galactic cosmic ray particles, were related to radiation or the distance from the auroral oval. These insights improve our ability to explain and understand population peaks, and should also motivate further studies on the effects of cosmic rays on plant chemistry and herbivore performance.     

Why do host‐deprived seed beetles ‘dump’ their eggs?

Abstract.  If host seeds are absent, females of the seed beetle Callosobruchus maculatus sometimes 'dump' eggs on unsuitable substrates, which causes complete larval mortality and decreases female lifespan. To understand the possible function of this behaviour, the present study examines genetic variation in dumping behaviour between and within populations. When deprived of hosts, females from an African population are much more prone to dump eggs than Asian females, most of which dump no eggs over their lifetimes. Egg dumping therefore cannot be explained as a simple, species-wide constraint imposed by the accumulation of mature oocytes. A transfer experiment tested the hypothesis that dumping eggs improves a female's ability to exploit the subsequent availability of seeds, perhaps by preventing a disruption of oocyte maturation. Contrary to prediction, the number of eggs laid after females are transferred to seeds is inversely related to the number dumped during deprivation. Two bidirectional selection experiments revealed heritable variation in egg-dumping behaviour within the African population. Deprived females from the dumper line dump more than twice as many eggs as do females from the nondumper line. Pre-adult development time is significantly longer in the nondumper line, which suggests that trade-offs with other fitness components could maintain variation in egg-laying behaviour within populations. The divergent responses to host availability by African and Asian females may represent a pleiotropic effect of similarly divergent responses to host quality.     

‘You are inferior!’ Revisiting the expressivist argument

According to the expressivist argument the choice to use biotechnologies to prevent the birth of individuals with specific disabilities is an expression of disvalue for existing people with this disability. The argument has stirred a lively debate and has recently received renewed attention. This article starts with presenting the expressivist argument and its core elements. It then goes on to present and examine the counter‐arguments before it addresses some aspects that have gained surprisingly little attention. The analysis demonstrates that the expressivist argument has a wide range of underpinnings and that counter‐arguments tend to focus on only a few of these. It also reveals an important aspect that appears to have been ignored, i.e., that people do not select foetuses based on chromosomes or other biological traits, but based on characteristics of living persons with specific disabilities. This makes it more difficult to undermine the claim that negative selection of foetuses expresses a disvaluing of persons with such disabilities. It leaves the expressivist argument with a strong bite still.     

Phylogenetic relatedness of co‐occurring waterbird communities: a test of Darwin's competition‐relatedness hypothesis

The competition–relatedness hypothesis of Darwin states that competition is greater among species that are phylogenetically closely‐related, and such species will tend to appear in separate communities (i.e. the species within communities will be phylogenetically overdispersed). Many studies have tested (and mainly refuted) this hypothesis for plant and bacterial communities. Results for the few studies with avian species are not conclusive. We tested Darwin's hypothesis for waterbirds using a set of open, artificial fish ponds in Doñana, south‐western Spain, that provide relatively homogeneous habitat where competition is likely to be intense. Monthly counts of 38 ponds (for 11 months, i.e. 418 censuses) recorded 76 bird species. Darwin's hypothesis predicted that species appearing in the same pond would be less related phylogenetically than expected if species occurred randomly across ponds and months according to the structure of the overall community across the entire pond complex. However, the waterbird community did not show a predominantly overdispersed pattern, suggesting that interspecific competition among phylogenetically related species was not the main force structuring communities. In contrast, the proportion of clustered communities was higher than expected throughout the annual cycle, indicating that related waterbirds tend to co‐occur on the same site, probably because they have similar microhabitat preferences. Clustering patterns were mainly driven by abundant and closely related duck species, and also by shorebirds. However, few individual pond communities remained significantly different from random after correction for multiple testing. Furthermore, the probability of co‐occurrence of a given species pair was negatively related to the phylogenetic distance between them. In conclusion, our study shows waterbird communities are mainly phylogenetically clustered or random, and do not support the competition‐relatedness hypothesis.     

Interaction of ‘toxic’ and ‘immunogenic’ A‐gliadin peptides with a membrane‐mimetic environment

Celiac disease (CD) is characterized by abnormally high concentrations of certain peptides in the small bowel. These peptides can be grouped in ‘toxic’ and ‘immunogenic’ classes, which elicit an innate immune response and an HLA‐mediated adaptive response, respectively. It is not clear on which molecular mechanisms responses to these different classes are based, but the 31–43 (P31–43) and the 56–68 (P56–68) A‐gliadin fragments are usually adopted as sequence representatives of toxic and immunogenic peptides, respectively. Here we report fluorescence experiments aiming to mimic the interaction of these peptides with the cell membrane surface by using sodium dodecyl sulphate (SDS) as a membrane‐mimetic medium. We show that P31–43 is able to bind SDS micelles in a way that resembles mixed micelle formation. On the other hand, no binding at all could be detected for P56–68. This different behaviour could be related to the paracellular or transcellular route through which gluten peptides may cross the intestinal epithelium, and open new insights into the pathogenetic mechanisms of CD. Copyright © 2009 John Wiley & Sons, Ltd.     

DEVELOPMENT OF A ‘BIPOLAR’ R‐INDEX1

A new ‘bipolar’ R‐index analysis was proposed and evaluated. Eighteen judges evaluated red color in eight wine samples by comparing each sample with the control. Judges indicated whether the sample had ‘more’, the 'same’, or ‘less’ red color than the control, and whether they were sure or unsure of their decision. Three computational methods were used to examine the results: the ‘traditional’ R‐index, the ‘bipolar’ R‐index (R_more or R_less) and the ‘weighted‐bipolar’ R‐index. While all three methods provided consistent results, the ‘bipolar’ R‐indices reflected bidirectional differences among the samples thus providing more information. A refinement to the computation (‘weighted‐bipolar’ R‐index) was an approach for eliminating the bias associated with overestimation of the sample size and accordingly changed some of the significance levels. Further research is currently underway to expand the scope and application of this method.     

Genetic variance for behavioural ‘predictability’ of stress response

Genetic factors underpinning phenotypic variation are required if natural selection is to result in adaptive evolution. However, evolutionary and behavioural ecologists typically focus on variation among individuals in their average trait values and seek to characterize genetic contributions to this. As a result, less attention has been paid to if and how genes could contribute towards within‐individual variance or trait ‘predictability’. In fact, phenotypic ‘predictability’ can vary among individuals, and emerging evidence from livestock genetics suggests this can be due to genetic factors. Here, we test this empirically using repeated measures of a behavioural stress response trait in a pedigreed population of wild‐type guppies. We ask (a) whether individuals differ in behavioural predictability and (b) whether this variation is heritable and so evolvable under selection. Using statistical methodology from the field of quantitative genetics, we find support for both hypotheses and also show evidence of a genetic correlation structure between the behavioural trait mean and individual predictability. We show that investigating sources of variability in trait predictability is statistically tractable and can yield useful biological interpretation. We conclude that, if widespread, genetic variance for ‘predictability’ will have major implications for the evolutionary causes and consequences of phenotypic variation.     

First report of ‘mining’ as a feeding behaviour among Australian manna‐feeding birds

The Forty‐spotted Pardalote Pardalotus quadragintus is an endangered songbird endemic to the forests of Tasmania, Australia. Forty‐spotted Pardalotes forage predominantly in the foliage of White (or Manna) Gums Eucalyptus viminalis for invertebrates, lerps (the protective coverings produced by psyllids) and manna, a crystallized exudate produced by certain Eucalyptus species. Although many Australian birds feed on manna, this study reports the first observations of birds actively stimulating manna production rather than feeding on it opportunistically. In light of these observations, we also compared rates of manna production across tree species and sizes, and quantified the relative importance of manna in nestling diet. Adult Forty‐spotted Pardalotes stimulated manna production by clipping leaf stalks with their bills, creating small incisions in the stem surface. We experimentally mimicked this behaviour and found that, in 53.7% of incisions of E. viminalis, manna flow was released within 3 days. However, none of the other three common tree species at our sites produced manna in response to the same experimental damage. There was no effect of tree size on manna production by E. viminalis. To determine the importance of manna and other food sources in nestling diet, we videotaped provisioning trips by adults to nests and surveyed food availability in E. viminalis foliage within territories. Manna was the most important food item, comprising 84.2% of identified food items provided to nestlings, and it was selected over 50 times more frequently than expected given its relative availability in the foliage. As a manna miner, the Forty‐spotted Pardalote is the first Australian bird to join the small number of bird species that mine sap or other exudates of trees. Their preference for manna as a food source, especially in nestling diet, provides an explanation for the species’ specialization on E. viminalis, the only manna‐producing tree at our sites. Our results suggest that E. viminalis forests provide critical food supply for developing nestlings, and that restoration of E. viminalis forests will be critical to the long‐term viability of Forty‐spotted Pardalote populations.     

Toll‐like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the ‘ghost of selection past’ and quantify the ‘drift debt’

Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a postbottlenecked population is challenging due to the potentially overriding effects of drift. Toll‐like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterized variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five of seven TLR loci were polymorphic, which is in sharp contrast to the low genomewide variation observed. However, standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR locus. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent‐based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the prebottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the ‘ghost of selection past’. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such ‘drift debt’ occurs when a gene pool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations.     

A SNP test to identify Africanized honeybees via proportion of ‘African’ ancestry

The honeybee, Apis mellifera, is the world's most important pollinator and is ubiquitous in most agricultural ecosystems. Four major evolutionary lineages and at least 24 subspecies are recognized. Commercial populations are mainly derived from subspecies originating in Europe (75–95%). The Africanized honeybee is a New World hybrid of A. m. scutellata from Africa and European subspecies, with the African component making up 50–90% of the genome. Africanized honeybees are considered undesirable for bee‐keeping in most countries, due to their extreme defensiveness and poor honey production. The international trade in honeybees is restricted, due in part to bans on the importation of queens (and semen) from countries where Africanized honeybees are extant. Some desirable strains from the United States of America that have been bred for traits such as resistance to the mite Varroa destructor are unfortunately excluded from export to countries such as Australia due to the presence of Africanized honeybees in the USA. This study shows that a panel of 95 single nucleotide polymorphisms, chosen to differentiate between the African, Eastern European and Western European lineages, can detect Africanized honeybees with a high degree of confidence via ancestry assignment. Our panel therefore offers a valuable tool to mitigate the risks of spreading Africanized honeybees across the globe and may enable the resumption of queen and bee semen imports from the Americas.     

The adaptive value of phenotypic floral integration

Floral integration has been deemed an adaptation to increase the benefits of animal pollination, yet no attempts have been made to estimate its adaptive value under natural conditions. Here, the variation in the magnitude and pattern of phenotypic floral integration and the variance-covariance structure of floral traits in four species of Rosaceae were examined. The intensity of natural selection acting on floral phenotypic integration was also estimated and the available evidence regarding the magnitude of floral integration reviewed. The species studied had similar degrees of floral integration, although significant differences were observed in their variance-covariance structure. Selection acted on subsets of floral traits (i.e. selection on intrafloral integration) rather than on the integration of the whole flower. Average integration was 20% and similar to the estimated mean value of flowering plants. The review indicated that flowering plants present lower integration than expected by chance. Numerical simulations suggest that this pattern may result from selection favouring intrafloral integration. Phenotypic integration at the flower level seems to have a low adaptive value among the species surveyed. Moreover, it is proposed that pollinator-mediated selection promotes the evolution of intrafloral integration.