Hybrid incompatibility is consistent with a hybrid origin of Heliconius heurippa Hewitson from its close relatives, Heliconius cydno Doubleday and Heliconius melpomene Linnaeus

Abstract Shared ancestral variation and introgression complicates the reconstruction of phylogenetic relationships among closely related taxa. Here we use overall genomic compatibility as an alternative estimate of species relationships in a group where divergence is rapid and genetic exchange is common. Heliconius heurippa, a butterfly species endemic to Colombia, has a colour pattern genetically intermediate between H. cydno and H. melpomene: its hindwing is nearly indistinguishable from that of H. melpomene and its forewing band is an intermediate phenotype between both species. This observation has lead to the suggestion that the pattern of H. heurippa arose through hybridization. We present a genetic analysis of hybrid compatibility in crosses between the three taxa. Heliconius heurippa x H. cydno and female H. melpomene x male H. heurippa yield fertile and viable F1 hybrids, but male H. melpomene x female H. heurippa crosses yield sterile F1 females. In contrast, Haldane's rule has previously been detected between H. melpomene and H cydno in both directions. Therefore, H. heurippa is most closely related to H. cydno, with some evidence for introgression of genes from H. melpomene. The results are compatible with the hypothesis of a hybrid origin for H. heurippa. In addition, backcrosses using F1 hybrid males provide evidence for a large Z(X)-chromosome effect on sterility and for recessive autosomal sterility factors as predicted by Dominance Theory.     

Macroevolutionary trends in the Dinosauria: Cope's rule

Cope's rule is the tendency for body size to increase over time along a lineage. A set of 65 phylogenetically independent comparisons, between earlier and later genera, show that Cope's rule applied in dinosaurs: later genera were on average about 25% longer than the related earlier genera to which they were compared. The tendency for size to increase was not restricted to a particular clade within the group, nor to a particular time within its history. Small lineages were more likely to increase in size, and large lineages more likely to decrease: this pattern may indicate an intermediate optimum body size, but can also be explained as an artefact of data error. The rate of size increase estimated from the phylogenetic comparisons is significantly higher than the rate seen across the fauna as a whole. This difference could indicate that within-lineage selection for larger size was opposed by clade selection favouring smaller size, but data limitations mean that alternative explanations (which we discuss) cannot be excluded. We discuss ways of unlocking the full potential usefulness of phylogenies for studying the dynamics of evolutionary trends.     

A structural alphabet for local protein structures: improved prediction methods

Three-dimensional protein structures can be described with a library of 3D fragments that define a structural alphabet. We have previously proposed such an alphabet, composed of 16 patterns of five consecutive amino acids, called Protein Blocks (PBs). These PBs have been used to describe protein backbones and to predict local structures from protein sequences. The Q16 prediction rate reaches 40.7% with an optimization procedure. This article examines two aspects of PBs. First, we determine the effect of the enlargement of databanks on their definition. The results show that the geometrical features of the different PBs are preserved (local RMSD value equal to 0.41 A on average) and sequence-structure specificities reinforced when databanks are enlarged. Second, we improve the methods for optimizing PB predictions from sequences, revisiting the optimization procedure and exploring different local prediction strategies. Use of a statistical optimization procedure for the sequence-local structure relation improves prediction accuracy by 8% (Q16 = 48.7%). Better recognition of repetitive structures occurs without losing the prediction efficiency of the other local folds. Adding secondary structure prediction improved the accuracy of Q16 by only 1%. An entropy index (Neq), strongly related to the RMSD value of the difference between predicted PBs and true local structures, is proposed to estimate prediction quality. The Neq is linearly correlated with the Q16 prediction rate distributions, computed for a large set of proteins. An "expected" prediction rate QE16 is deduced with a mean error of 5%.     

A biogeographic pattern in sparrow bill morphology: parallel adaptation to tidal marshes

The study of ecological convergence, the evolution of similar traits on multiple occasions in response to similar conditions, is a powerful method for developing and testing adaptive hypotheses. However, despite the great attention paid to geographic variation and the foraging ecology of birds, surprisingly few cases of convergent or parallel feeding adaptations have been adequately documented. In this study, we document a biogeographic pattern of parallel bill morphology across 10 sparrow taxa endemic to tidal marshes. All North American tidal marsh sparrows display parallel differentiation from close relatives in other habitats, suggesting that selection on bill morphology is strong. Relative to their body mass, tidal marsh sparrows have longer, thinner bills than their non-tidal marsh counterparts, which is likely an adaptation for consuming more invertebrates and fewer seeds, as well as for probing in sediment crevices to capture prey. Published data on tidal marsh food resources and diet of the relevant taxa support this hypothesis. This morphological differentiation is most pronounced between sister taxa with the greatest estimated divergence times, but is found even in taxa that show little or no structure in molecular genetic markers. We, therefore, speculate that tidal marsh ecosystems are likely settings for ecological speciation.     

Changes of enzyme activity in lipid signaling pathways related to substrate reordering

The static fluid mosaic model of biological membranes has been progressively complemented by a dynamic membrane model that includes phospholipid reordering in domains that are proposed to extend from nanometers to microns. Kinetic models for lipolytic enzymes have only been developed for homogeneous lipid phases. In this work, we develop a generalization of the well-known surface dilution kinetic theory to cases where, in a same lipid phase, both domain and nondomain phases coexist. Our model also allows understanding the changes in enzymatic activity due to a decrease of free substrate concentration when domains are induced by peptides. This lipid reordering and domain dynamics can affect the activity of lipolytic enzymes, and can provide a simple explanation for how basic peptides, with a strong direct interaction with acidic phospholipids (such as beta-amyloid peptide), may cause a complex modulation of the activities of many important enzymes in lipid signaling pathways.     

An approach to the residence time distribution for stochastic multi-compartment models

Stochastic compartmental models are widely used in modeling processes such as drug kinetics in biological systems. This paper considers the distribution of the residence times for stochastic multi-compartment models, especially systems with non-exponential lifetime distributions. The paper first derives the moment generating function of the bivariate residence time distribution for the two-compartment model with general lifetimes and approximates the density of the residence time using the saddlepoint approximation. Then, it extends the distributional approach to the residence time for multi-compartment semi-Markov models combining the cofactor rule for a single destination and the analytic approach to the two-compartment model. This approach provides a complete specification of the residence time distribution based on the moment generating function and thus facilitates an easier calculation of high-order moments than the approach using the coefficient matrix. Applications to drug kinetics demonstrate the simplicity and usefulness of this approach.     

Role of sexual and natural selection in evolution of body size and shape: a phylogenetic study of morphological radiation in grouse

We use standardized independent contrasts (SICs) to elucidate the effect of ecology and mating systems on morphological radiation in grouse. The analysis of SICs for 38 skeletal measurements from 20 taxa, showed that changes in mating system had a significant effect on body size of both sexes. Sexual size dimorphism in grouse is consistent with Rensch's rule; the slope of the regression of male vs. female size SICs was 1.4, significantly >1. Changes in habitat were associated with accelerated rates of evolution of body proportions. SICs for male and female scores of size independent factors were directly proportional to each other (slope = 1), indicating extreme similarities between male and female ecology. Females, however, were better adapted to longer, more energy efficient flight than males. Size independent morphological differences among grouse are adaptive and are related to the differences in habitat and foraging behaviour among the species.     

A general model for the evolution of mutualisms

The evolution of mutualisms presents a puzzle. Why does selection favour cooperation among species rather than cheaters that accept benefits but provide nothing in return? Here we present a general model that predicts three key factors will be important in mutualism evolution: (i) high benefit to cost ratio, (ii) high within‐species relatedness and (iii) high between‐species fidelity. These factors operate by moderating three types of feedback benefit from mutualism: cooperator association, partner‐fidelity feedback and partner choice. In defining the relationship between these processes, our model also allows an assessment of their relative importance. Importantly, the model suggests that phenotypic feedbacks (partner‐fidelity feedback, partner choice) are a more important explanation for between‐species cooperation than the development of genetic correlations among species (cooperator association). We explain the relationship of our model to existing theories and discuss the empirical evidence for our predictions.     

The evolution of sex-specific grandparental harm

Recent empirical studies indicate that grandparents favour some categories of grandchildren over others. Here, we expand the previous theoretical foundation for this finding and show that grandchild-harming phenotypes are predicted to evolve by ‘sexually antagonistic zygotic drive (SA-zygotic drive) of the sex chromosomes’. We use the logic of Hamilton''s rule to develop a new ‘no-cost-to-self nepotism rule’ that greatly simplifies the determination of the invasion criteria for mutations that cause grandparents to harm grandchildren. We use this theory to generate predictions that distinguish SA-zygotic drive from theory based solely on paternity assurance. The major diagnostic prediction is that grandmothers, and to a lesser degree grandfathers, will evolve grandson-harming phenotypes that reduce the level of sib competition experienced by their more closely related granddaughters, especially in their sons'' families. This prediction is supported by data from recent studies showing (i) grandmothers invest more in granddaughters than grandsons, and counterintuitively, (ii) paternal grandmothers reduce the survival of their grandsons. We conclude that SA-zygotic drive is plausibly operating in humans via sexually antagonistic grandparental care.     

Simulation of Rapoport's rule for latitudinal species spread

Rapoport's rule claims that latitudinal ranges of plant and animal species are generally smaller at low than at high latitudes. However, doubts as to the generality of the rule have been expressed, because studies providing evidence against the rule are more numerous than those in support of it. In groups for which support has been provided, the trend of increasing latitudinal ranges with latitude is restricted to or at least most distinct at high latitudes, suggesting that the effect may be a local phenomenon, for example the result of glaciations. Here we test the rule using two models, a simple one-dimensional one with a fixed number of animals expanding in a northern or southerly direction only, and the evolutionary/ecological Chowdhury model using birth, ageing, death, mutation, speciation, prey-predator relations and food levels. Simulations with both models gave results contradicting Rapoport's rule. In the first, latitudinal ranges were roughly independent of latitude, in the second, latitudinal ranges were greatest at low latitudes, as also shown empirically for some well-studied groups of animals.