Ashmole's hypothesis and the latitudinal gradient in clutch size

One enduring priority for ecologists has been to understand the cause(s) of variation in reproductive effort among species and localities. Avian clutch size generally increases with increasing latitude, both within and across species, but the mechanism(s) driving that pattern continue to generate hypotheses and debate. In 1961, a Ph.D. student at Oxford University, N. Philip Ashmole, proposed the influential hypothesis that clutch size varies in direct proportion to the seasonality of resources available to a population. Ashmole's hypothesis has been widely cited and discussed in the ecological literature. However, misinterpretation and confusion has been common regarding the mechanism that underlies Ashmole's hypothesis and the testable predictions it generates. We review the development of well-known hypotheses to explain clutch size variation with an emphasis on Ashmole's hypothesis. We then discuss and clarify sources of confusion about Ashmole's hypothesis in the literature, summarise existing evidence in support and refutation of the hypothesis, and suggest some under-utilised and novel approaches to test Ashmole's hypothesis and gain an improved understanding of the mechanisms responsible for variation in avian clutch size and fecundity, and life-history evolution in general.     

The evolution of floral sonication,a pollen foraging behavior used by bees (Anthophila)

Over 22,000 species of biotically pollinated flowering plants, including some major agricultural crops, depend primarily on bees capable of floral sonication for pollination services. The ability to sonicate (“buzz”) flowers is widespread in bees but not ubiquitous. Despite the prevalence of this pollinator behavior and its importance to natural and agricultural systems, the evolutionary history of floral sonication in bees has not been previously studied. Here, we reconstruct the evolutionary history of floral sonication in bees by generating a time‐calibrated phylogeny and reconstructing ancestral states for this pollen extraction behavior. We also test the hypothesis that the ability to sonicate flowers and thereby efficiently access pollen from a diverse assemblage of plant species, led to increased diversification among sonicating bee taxa. We find that floral sonication evolved on average 45 times within bees, possibly first during the Early Cretaceous (100–145 million years ago) in the common ancestor of bees. We find that sonicating lineages are significantly more species rich than nonsonicating sister lineages when comparing sister clades, but a probabilistic structured rate permutation on phylogenies approach failed to support the hypothesis that floral sonication is a key driver of bee diversification. This study provides the evolutionary framework needed to further study how floral sonication by bees may have facilitated the spread and common evolution of angiosperm species with poricidal floral morphology.     

Age-specific reproductive success: evidence for the selection hypothesis

Age-specific reproductive success has been demonstrated in many species. Three hypotheses have been raised to explain this general phenomenon: the experience hypothesis based on age-specific reproductive experience, the effort hypothesis based on age-specific reproductive effort, and the selection hypothesis based on progressive disappearance of phenotypes due to variation in individual productivity and survival. We used data from a long-term study of Leach's storm-petrels (Oceanodroma leucorhoa) to present a single test of mutually exclusive predictions about the relationship between early breeding success and longevity. There should be no correlation between early breeding success and longevity under the experience hypothesis, a negative correlation under the effort hypothesis, and a positive correlation under the selection hypothesis. We found a significant (P < 0.0001) positive relationship between success in the first two breeding attempts and longevity in this population of long-lived seabirds, strongly suggesting that low-productivity parents were also less likely to survive early breeding. These data provide some of the strongest support to date for the selection hypothesis.     

Intraspecific sexual selection on a speciation trait, male coloration, in the Lake Victoria cichlid Pundamilia nyererei

The haplochromine cichlids of Lake Victoria constitute a classical example of explosive speciation. Extensive intra- and interspecific variation in male nuptial coloration and female mating preferences, in the absence of postzygotic isolation between species, has inspired the hypothesis that sexual selection has been a driving force in the origin of this species flock. This hypothesis rests on the premise that the phenotypic traits that underlie behavioural reproductive isolation between sister species diverged under sexual selection within a species. We test this premise in a Lake Victoria cichlid, by using laboratory experiments and field observations. We report that a male colour trait, which has previously been shown to be important for behavioural reproductive isolation between this species and a close relative, is under directional sexual selection by female mate choice within this species. This is consistent with the hypothesis that female choice has driven the divergence in male coloration between the two species. We also find that male territoriality is vital for male reproductive success and that multiple mating by females is common.     

The rise of the hominids as an adaptive shift in fallback foods: plant underground storage organs (USOs) and australopith origins

We propose that a key change in the evolution of hominids from the last common ancestor shared with chimpanzees was the substitution of plant underground storage organs (USOs) for herbaceous vegetation as fallback foods. Four kinds of evidence support this hypothesis: (1) dental and masticatory adaptations of hominids in comparison with the African apes; (2) changes in australopith dentition in the fossil record; (3) paleoecological evidence for the expansion of USO-rich habitats in the late Miocene; and (4) the co-occurrence of hominid fossils with root-eating rodents. We suggest that some of the patterning in the early hominid fossil record, such as the existence of gracile and robust australopiths, may be understood in reference to this adaptive shift in the use of fallback foods. Our hypothesis implicates fallback foods as a critical limiting factor with far-reaching evolutionary effects. This complements the more common focus on adaptations to preferred foods, such as fruit and meat, in hominid evolution.     

Walter’s two-layer hypothesis revisited: back to the roots!

Walter (Jahrb Wiss Bot 87:750–860, 1939) proposed a two-layer hypothesis, an equilibrium explanation for coexistence of savanna trees and grasses. This hypothesis relies on vertical niche partitioning and assumed that grasses are more water-use efficient than trees and use subsurface water while trees also have access to deeper water sources. Thus, in open savannas, grasses were predicted to predominate because of their water use efficiency and access to subsurface water. This hypothesis has been a prominent part of the savanna literature since first proposed. We review the literature on Walter’s hypothesis and reconsider his original intentions. Walter intended this hypothesis to be restricted to dry savannas. In his opinion, mesic and humid savannas were controlled by biotic factors and disturbances. We surveyed the global savanna literature for records of vertical niche partitioning by grasses and trees. We find that, within the scope of Walter’s original intentions, this hypothesis works remarkably well, and in some cases is appropriate for deserts as well as for dry temperate systems and even some mesic savannas.     

Major histocompatibility complex variability in the clonal Amazon molly,Poecilia formosa: is copy number less important than genotype?

The evolution of sex is still a major unsolved puzzle in biology. One of the most promising theoretical models to answer this question is the Red Queen hypothesis. The Red Queen hypothesis proposes a fast adaptation of pathogens to common genotypes and therefore a negative frequency-dependent selection against common genotypes. Clonal organisms should be especially endangered when co-occurring with closely related sexual species. In this context, major histocompatibility (MHC) genes have been discussed to be auspicious candidates that could provide the genetic basis on which selection for immune competence could act. In this study, we investigated MHC variability in a clonal teleost fish: the Amazon molly, Poecilia formosa . The Amazon molly is an ideal candidate to test the Red Queen hypothesis as it is a clonal species but co-occurs with a closely related sexual species and should therefore be especially susceptible to pathogen infection. We found that allele numbers did in general not differ between sexual and clonal 'species' but that genotypic variability is reduced in the clonally reproducing fish, especially in the polyploids. We conclude that in clonal organisms, genotype frequency might be more important for immune competence than MHC allele number. Amazon mollies and their co-occurring parental species clearly fulfil a prerequisite of the Red Queen hypothesis and should therefore provide an ideal system to experimentally test this basic principle probably underlying the evolution of sex.     

Release from sheep-grazing appears to put some heart back into upland vegetation: A comparison of nutritional properties of plant species in long-term grazing experiments

Rewilding or wilding is a popularised means for enhancing the conservation value of marginal land. In the British uplands, it will involve a reduction, or complete removal, of livestock grazing (sheep), based on the belief that grazing has reduced plant species diversity, the ‘Wet Desert’ hypothesis. The hope is that if livestock is removed, diversity will recover. If true, we hypothesise that the species extirpated/reduced by grazing and then recover on its removal would more nutritious compared to those that persisted. We test this hypothesis at Moor House National Nature Reserve (North-Pennines), where seven sets of paired plots were established between 1953 and 1967 to compare ungrazed/sheep-grazed vegetation. Within these plot-pairs, we compared leaf properties of seven focal species that occurred only, or were present in much greater abundance, in the absence of grazing to those of 10 common species that were common in both grazed and ungrazed vegetation. Each sample was analysed for macro-nutrients, micro-nutrients, digestibility, palatability and decomposability. We ranked the species with respect to 22 variables based on effect size derived from Generalised Linear Modelling (GLM) and compared species using a Principal Components Analysis. We also assessed changes in abundance of the focal species through time using GLMs. Our results support the ‘Wet Desert’ hypothesis, that is, that long-term sheep grazing has selectively removed/reduced species like our focal ones and on recovery, they were more nutritious (macro-nutrients, some micro-nutrients) palatable, digestible and decomposable than common species. Measured changes in abundance of the focal species suggest that their recovery will take 10–20 years in blanket bog and 60 years in high-altitude grasslands. Collectively, these results suggest that sheep grazing has brought about biotic homogenization, and its removal in (re)wilding schemes will reverse this process eventually! The ‘white woolly maggots’ have eaten at least part of the heart out of the highlands/uplands, and it will take some time for recovery.     

Efficient inference on known phylogenetic trees using Poisson regression

MOTIVATION: We suggest the use of Poisson regression for time inference and hypothesis testing on a bifurcating Phylogenetic tree with known topology. This method is computationally simple and naturally accommodates variable substitution rates across different sites, without requiring the estimation of these rates. We identify the assumptions under which this is a maximum-likelihood inference approach and show that in some realistic situations--in particular, when the probability of repeated mutation within each branch of the tree is small--these assumptions hold with high probability. RESULTS: Our motivating domain is human mitochondrial DNA trees, and we illustrate our method on a problem of estimating the time to most recent common ancestor of all non-African mtDNA, using publicly available data. We test for molecular clock violations using multiple comparisons, and conclude that the global molecular clock hypothesis cannot be rejected based on these data.     

Asthma: a disorder of adrenergic receptors?

For the past 20 years, the hypothesis that bronchial asthma represents an imbalance between deficient activity of the beta-adrenergic receptor pathway and/or enhanced activity of alpha-adrenergic/muscarinic cholinergic pathways in the regulation of airway smooth muscle has been a popular idea. Although some evidence supports this hypothesis, direct proof of its validity has been elusive. Concepts regarding the pathobiology of asthma have shifted from a focus on changes in smooth muscle per se to the prominent inflammatory nature of this disorder. We review some of the evolving information regarding the pathogenesis of this disorder and discuss how altered neurohormonal regulation of key inflammatory cells may contribute to the asthmatic condition.     

Why are female color polymorphisms rare in territorial damselflies?

In nonterritorial damselflies, females often come in multiple color morphs, perhaps because females with rare colors experience reduced sexual harassment, and thus have a frequency‐dependent fitness advantage, compared to females of the most common color morph, but such polymorphisms are rare in territorial species. We consider three hypotheses to explain the rarity of female color polymorphisms in territorial species: (a) misdirected male aggression, (b) poor male mate recognition, and (c) low mating harassment rates. The first hypothesis has some empirical support, and can account for the absence of andromorphs (i.e., females that resemble males), but does not explain the absence of multiple heteromorphs. We tested the second hypothesis by presenting females of two novel color morphs (green‐ or red‐banded abdomens) to territorial male Hetaerina capitalis. Females of both novel color morphs elicited fewer sexual responses than control females, and the red morph occasionally elicited aggressive responses. These results indicate that novel female color morphs would experience reduced mating harassment in this species, contradicting the hypothesis that male mate recognition is too poorly developed to reduce harassment of novel female morphs. By process of elimination, the third hypothesis, that harassment rates are too low in territorial species to provide rare female morphs a fitness advantage, is favored, but remains untested. Our findings also suggest that the common practice of color‐marking odonates for behavioral research is likely to interfere with mate choice, as has long been known to be the case in birds.     

EVOLUTION OF HAPLODIPLOIDY IN DERMANYSSINE MITES (ACARI: MESOSTIGMATA)

Haplodiploidy, a widespread phenomenon in which males are haploid and females are diploid, can be caused by a number of different underlying genetic systems. In the most common of these, arrhenotoky, males arise from unfertilized eggs, whereas females arise from fertilized eggs. In another system, pseudoarrhenotoky, males arise from fertilized eggs, but they eliminate the paternal genome at some point prior to spermatogenesis, with the consequence that they do not pass this genome to their offspring. In 1931 Schrader and Hughes-Schrader suggested that arrhenotoky arises through a series of stages involving pseudoarrhenotokous systems such as those found in many scale insects (Homoptera: Coccoidea), however, their hypothesis has been largely ignored. We have used a phylogenetic analysis of 751 base pairs of 28S rDNA from a group of mites (Mesostigmata: Dermanyssina) that contains arrhenotokous, pseudoarrhenotokous, and ancestrally diplodiploid members to test this hypothesis. Neighbor-joining, maximum-parsimony, and maximum-likelihood methods all indicate that the arrhenotokous members of this group form a clade that arose from a pseudoarrhenotokous ancestor, rather than directly from a diplodiploid one. This provides unequivocal support for the hypothesis of Schrader and Hughes-Schrader. The wider implications of this result for the evolution of uniparental genetic systems are discussed.     

The contribution of rare species to community phylogenetic diversity across a global network of forest plots

Niche differentiation has been proposed as an explanation for rarity in species assemblages. To test this hypothesis requires quantifying the ecological similarity of species. This similarity can potentially be estimated by using phylogenetic relatedness. In this study, we predicted that if niche differentiation does explain the co-occurrence of rare and common species, then rare species should contribute greatly to the overall community phylogenetic diversity (PD), abundance will have phylogenetic signal, and common and rare species will be phylogenetically dissimilar. We tested these predictions by developing a novel method that integrates species rank abundance distributions with phylogenetic trees and trend analyses, to examine the relative contribution of individual species to the overall community PD. We then supplement this approach with analyses of phylogenetic signal in abundances and measures of phylogenetic similarity within and between rare and common species groups. We applied this analytical approach to 15 long-term temperate and tropical forest dynamics plots from around the world. We show that the niche differentiation hypothesis is supported in six of the nine gap-dominated forests but is rejected in the six disturbance-dominated and three gap-dominated forests. We also show that the three metrics utilized in this study each provide unique but corroborating information regarding the phylogenetic distribution of rarity in communities.     

The ubiquitous nature of epistasis in determining susceptibility to common human diseases

There is increasing awareness that epistasis or gene-gene interaction plays a role in susceptibility to common human diseases. In this paper, we formulate a working hypothesis that epistasis is a ubiquitous component of the genetic architecture of common human diseases and that complex interactions are more important than the independent main effects of any one susceptibility gene. This working hypothesis is based on several bodies of evidence. First, the idea that epistasis is important is not new. In fact, the recognition that deviations from Mendelian ratios are due to interactions between genes has been around for nearly 100 years. Second, the ubiquity of biomolecular interactions in gene regulation and biochemical and metabolic systems suggest that relationship between DNA sequence variations and clinical endpoints is likely to involve gene-gene interactions. Third, positive results from studies of single polymorphisms typically do not replicate across independent samples. This is true for both linkage and association studies. Fourth, gene-gene interactions are commonly found when properly investigated. We review each of these points and then review an analytical strategy called multifactor dimensionality reduction for detecting epistasis. We end with ideas of how hypotheses about biological epistasis can be generated from statistical evidence using biochemical systems models. If this working hypothesis is true, it suggests that we need a research strategy for identifying common disease susceptibility genes that embraces, rather than ignores, the complexity of the genotype to phenotype relationship.     

Risk-sensitive fertility: The variance compensation hypothesis

Two conditions are sufficient to indicate the need for risk-sensitive, adaptive analysis: (i) the outcomes of a behavior must be unpredictable to some degree and (ii) the relationship between outcomes and their value (in terms of fitness or utility) must be nonlinear. We argue that these conditions are common, and develop a general model for the analysis of risk-sensitive fertility behavior when long-term reproductive outcomes are unpredictable. We show that unpredictability is likely to have a patterned effect on fertility behavior, beyond adjustment for expected or average mortality, and we analyze the conditions under which that effect will be to promote or dampen fertility (positive or negative variance compensation, respectively). We then describe the implications of this variance compensation hypothesis (VCH) for the analysis of demographic transitions, agricultural intensification, fertility differences in natural-fertility populations, and clutch size. We conclude by lamenting that data are lacking to test the VCH, probably because it has not been appreciated that there can be patterned and effective behavioral adjustments to stochastic features of the environment.     

Alpha-tocopheryl succinate epitomizes a compound with a shift in biological activity due to pro-vitamin-to-vitamin conversion

With the advent of the third millennium, a number of pathologies have been eradicated or taken under control. However, the incidences, of cancer and atherosclerosis, the two most common causes of death in developed countries, have increased or, in some instances, only stagnated. Therefore there has been an intensive search for agents effective against such life-threatening conditions. Accordingly, the potential anti-atherogenic activity of vitamin E analogs has been studied extensively. Interestingly, recent reports strongly suggest that certain vitamin E analogs, represented in particular by alpha-tocopheryl succinate (alpha-TOS), also possess anti-neoplastic activity. In this communication, we review our current understanding of the molecular basis for these double effects of alpha-TOS and propose a testable hypothesis, according to which this semi-synthetic analog exerts both anti-atherogenic and anti-neoplastic activities. We propose that the prevalence of each activity depends on the actual form of the vitamin E analog. That is, the conversion of the pro-vitamin E form, alpha-TOS, to the corresponding vitamin form, alpha-tocopherol, makes this anti-neoplastic agent active against inflammatory diseases like atherosclerosis.     

Fluoride: interaction with chemical mutagens in Drosophila

Simultaneous feeding of sodium fluoride and some chemical mutagens to Drosophila has been reported to reduce the yield of induced mutations compared with feeding the mutagens alone. This observation has been interpreted as a genuine case of antimutagenesis in which fluoride specifically inhibits the induction of chromosome breaks. An alternative hypothesis is that the presence of fluoride inhibits the uptake of the mutagen solutions, producing the same effect as an antimutagen, but for a trivial reason. We have tested this hypothesis using radioactive labelled sucrose to measure the uptake of test solutions. The results show that differential uptake can account for the "antimutagenic" effects reported in Drosophila. Comparison of recessive lethal frequencies induced by Trenimon and PDT do not support the hypothesis that fluoride has any genuine antimutagenic action. Antimutagenic effects of fluoride have been reported in other systems. We cannot exclude the possibility of some genuine effects but we consider that these reports should be critically re-examined in the light of our present findings.     

Individual female common cuckoos Cuculus canorus lay constant egg types but egg appearance cannot be used to assign eggs to females

Females of the obligate brood parasitic common cuckoo Cuculus canorus are assumed to lay eggs of consistent colour and pattern and egg characteristics have been used to separate between different individuals. We tested the "constant egg-type hypothesis" in blind tests using test persons who grouped cuckoo eggs into "potential clutches" based on similarity in appearance. A correct classification of eggs laid by known (radiotagged) females supported the hypothesis. However, comparisons between maternity based on visual assessments and DNA-based parentage analyses revealed rather poor concordance between the two methods. Our findings indicate that egg characteristics cannot be used to separate between cuckoo females, even if they lay eggs with constant appearance. The reason is probably that there are only small or negligible variations in egg appearance between some females like mothers and daughters or other closely related individuals.     

Phylogenetic analysis of 1.5 Mbp and platypus EST data refute the Marsupionta hypothesis and unequivocally support Monotremata as sister group to Marsupialia/Placentalia

The extant mammalian groups Monotremata, Marsupialia and Placentalia are, according to the 'Theria' hypothesis, traditionally classified into two subclasses. The subclass Prototheria includes the monotremes and subclass Theria marsupials and placental mammals. Based on some morphological and molecular data, an alternative proposition, the Marsupionta hypothesis, favours a sister group relationship between monotremes and marsupials to the exclusion of placental mammals. Phylogenetic analyses of single genes and even multiple gene alignments have not yet been able to conclusively resolve this basal mammalian divergence. We have examined this problem using one data set composed of expressed sequence tags (EST) and another containing 1 510 509 nucleotide (nt) sites from 1358 inferred cDNA genomic sequences. All analyses of the concatenated sequences unambiguously supported the Theria hypothesis. The Marsupionta hypothesis was rejected with high statistical confidence from both data sets. In spite of the strong support for Theria, a non-negligible number of single genes supported either of the two alternative hypotheses. The divergence between monotremes and therian mammals was estimated to have taken place 168–178 Mya, a dating compatible with the fossil record. Considering the long common evolutionary branch of therians, it is surprising that sequence data from many thousand amino acid sites were needed to conclusively resolve their relationship to monotremes. This finding draws attention to other mammalian divergences that have been taken as unequivocally settled based on much smaller alignments. EST data provide a comprehensive random sample of protein coding sequences and an economic way to produce large amounts of data for phylogenetic analysis of species for which genomic sequences are not yet available.     

The quality preserving database: a computational framework for encouraging collaboration, enhancing power and controlling false discovery

The common scenario in computational biology in which a community of researchers conduct multiple statistical tests on one shared database gives rise to the multiple hypothesis testing problem. Conventional procedures for solving this problem control the probability of false discovery by sacrificing some of the power of the tests. We suggest a scheme for controlling false discovery without any power loss by adding new samples for each use of the database and charging the user with the expenses. The crux of the scheme is a carefully crafted pricing system that fairly prices different user requests based on their demands while keeping the probability of false discovery bounded. We demonstrate this idea in the context of HIV treatment research, where multiple researchers conduct tests on a repository of HIV samples.