The phylogenetic position of early hexapod lineages: morphological data contradict molecular data

Abstract. A review of different studies on the phylogenetic relationships of the early Hexapoda lineages shows that analyses based on molecular sequence data have led to labile and sometimes incongruous results, introducing doubt as to the reliability of the cladograms as a whole. In a recent analysis using molecular data, the Collembola, usually considered as early branching hexapods, appear to occupy a position outside the assemblage of Crustacea and Insecta, leading to the rejection of the traditional view of hexapod monophyly. However, many morphological features, as well as the results of cladistic analyses based on morphological and developmental information, contradict these conclusions. More generally, it appears that in the present state of the analytical strategies, hypotheses concerning arthropod phylogenies obtained from morphological and developmental criteria and combined analyses involving molecular and morphological data provide more reliable results than those generated by molecular information alone.     

Transmembrane topography of nicotinic acetylcholine receptor: immunochemical tests contradict theoretical predictions based on hydrophobicity profiles

In our preceding paper [Ratnam, M., Sargent, P. B., Sarin, V., Fox, J. L., Le Nguyen, D., Rivier, J., Criado, M., & Lindstrom, J. (1986) Biochemistry (preceding paper in this issue)], we presented results from peptide mapping studies of purified subunits of the Torpedo acetylcholine receptor which suggested that the sequence beta 429-441 is on the cytoplasmic surface of the receptor. Since this finding contradicts earlier theoretical models of the transmembrane structure of the receptor, which placed this sequence of the beta subunit on the extracellular surface, we investigated the location of the corresponding sequence (389-408) and adjacent sequences of the alpha subunit by a more direct approach. We synthesized peptides including the sequences alpha 330-346, alpha 349-364, alpha 360-378, alpha 379-385, and alpha 389-408 and shorter parts of these peptides. These peptides corresponded to a highly immunogenic region, and by using 125I-labeled peptides as antigens, we were able to detect in our library of monoclonal antibodies to alpha subunits between two and six which bound specifically to each of these peptides, except alpha 389-408. We obtained antibodies specific for alpha 389-408 both from antisera against the denatured alpha subunit and from antisera made against the peptide. These antibodies were specific to alpha 389-396. In binding assays, antibodies specific for all of these five peptides bound to receptor-rich membrane vesicles only after permeabilization of the vesicles to permit access of the antibodies to the cytoplasmic surface of the receptors, suggesting that the receptor sequences which bound these antibodies were located on the intracellular side of the membrane. Electron microscopy using colloidal gold to visualize the bound antibodies was used to conclusively demonstrate that all of these sequences are exposed on the cytoplasmic surface of the receptor. These results, along with our previous demonstration that the C-terminal 10 amino acids of each subunit are exposed on the cytoplasmic surface, show that the hydrophobic domain M4 (alpha 409-426), previously predicted from hydropathy profiles to be transmembranous, does not, in fact, cross the membrane. Further, these results show that the putative amphipathic transmembrane domain M5 (alpha 364-399) also does not cross the membrane. Our results thus indicate that the transmembrane topology of a membrane protein cannot be deduced strictly from the hydropathy profile of its primary amino acid sequence. We present a model for the transmembrane orientation of receptor subunit polypeptide chains which is consistent with current data.     

Regulatory links between imprinted genes: evolutionary predictions and consequences

Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.     

The extended evolutionary synthesis: its structure,assumptions and predictions

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis'' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.     

Surprising evolutionary predictions from enhanced ecological realism

A focus on the eco-evolutionary feedback continually operating between a population's evolution and its environment helps to appreciate the generality of ESS theory. Here we illustrate, through a sequence of four examples, how respecting such feedback in the evolutionary dynamics of quantitative traits may result in qualitatively unexpected outcomes. Reviewing existing insights and complementing these with new results, we show (1) that evolutionary matrix games are fundamentally degenerate and allow a natural unfolding, (2) that selection-driven extinction may not be rare in nature, (3) that evolutionary epidemiology should not rely on R0 maximization, and (4) why the occurrence of Hardy-Weinberg proportions generically requires an evolutionary explanation.     

Plant tolerance and resistance in food webs: community-level predictions and evolutionary implications

While evolutionary ecologists emphasize different ways in which plants can evolutionarily respond to herbivory, such as resistance or tolerance, community ecology has lagged in its understanding of how these different plant traits can influence interactions, abundance, composition, and diversity within more complex food webs. In this paper, we present a series of models comparing community level outcomes when plants either resist or tolerate herbivory. We show that resistance and tolerance can lead to very different outcomes. A particularly important result is that resistant species should often coexist locally with other, less resistant competitors, whereas tolerant species should not be able to coexist locally with less tolerant competitors, although priority effects allow them to coexist regionally. We also use these models to suggest some insights into the evolution of these traits within more complex communities. We emphasize how understanding the differential effects of plant tolerance and resistance in food webs provides greater appreciation of a variety of empirical patterns that heretofore have appeared enigmatic. This revised version was published online in July 2006 with corrections to the Cover Date.     

SplitsTree: analyzing and visualizing evolutionary data

MOTIVATION: Real evolutionary data often contain a number of different and sometimes conflicting phylogenetic signals, and thus do not always clearly support a unique tree. To address this problem, Bandelt and Dress (Adv. Math., 92, 47-05, 1992) developed the method of split decomposition. For ideal data, this method gives rise to a tree, whereas less ideal data are represented by a tree-like network that may indicate evidence for different and conflicting phylogenies. RESULTS: SplitsTree is an interactive program, for analyzing and visualizing evolutionary data, that implements this approach. It also supports a number of distances transformations, the computation of parsimony splits, spectral analysis and bootstrapping.      

Disobedient epiphytes: colonization and extinction rates in a metapopulation of Lepanthes rupestris (Orchidaceae) contradict theoretical predictions based on patch connectivity

The metapopulation concept is widely established in population biology. It predicts that the likelihood of colonization of an empty patch is positively correlated with its connectivity, because colonizers from occupied patches will be more likely to reach an empty patch if they are closer to it. Another prediction is that the likelihood of extinction of an occupied patch will be negatively correlated with its connectivity to other patches, as the occupied patch can be ‘reinforced’ by immigrants from patches that are close by. We tested these predictions using an extensive data set for an epiphytic orchid, Lepanthes rupestris from Puerto Rico. Our data did not support the first prediction, but we found that the likelihood of extinction is negatively correlated with patch connectivity. We hypothesize that this might be because most orchid seeds are wind dispersed and seeds that do not fall immediately below the mother plant are uniformly distributed after a steep leptokurtic distribution. We predict that taxa with similar seed and gene flow characteristics should show similar patterns in the association between colonization/extinction rates and patch connectivity. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 598–606.     

Animal cognition: monkey looks contradict Hume

Wild rhesus monkeys have been found to attend to causal anomalies, suggesting that they make inferences about possible and impossible physical transformations in the absence of direct relevant experience.     

A role for evolutionary predictions in gene isolation and characterization studies

Studies of the evolutionary history of gene families can provide important insight into the processes leading to functional conservation or divergence among orthologs and paralogs. While the pattern of relationships among family members may be difficult to predict prior to an analysis, there are several expectations that should be met that can provide evolutionary verifications for gene isolation and characterization studies. In this report, it is shown that a recently described jasmonic acid caboxyl methyltransferase (JMT) sequence fromCapsicum annuum L. (hot pepper) fails to satisfy several evolutionary predictions. Specifically, the hot pepper sequence is more closely related to someArabidopsis thaliana (L.) Heynh. strains than are other strains ofA. thaliana or its close relativeBrassica campestris L. In addition, the level of divergence of hot pepper andA. thaliana JMT is more than ten times lower than expected from the levels of divergence of their mitochondrial and plastid sequences. Finally, attempts to PCR amplify JMT from hot pepper DNA were unsuccessful. In light of these empirical results, the identity of the putative hot pepper JMT sequence is called into question and highlights the need for phylogenetic perspectives even for functional studies.     

Genomewide predictions from maize single-cross data

Maize (Zea mays L.) breeders evaluate many single-cross hybrids each year in multiple environments. Our objective was to determine the usefulness of genomewide predictions, based on marker effects from maize single-cross data, for identifying the best untested single crosses and the best inbreds within a biparental cross. We considered 479 experimental maize single crosses between 59 Iowa Stiff Stalk Synthetic (BSSS) inbreds and 44 non-BSSS inbreds. The single crosses were evaluated in multilocation experiments from 2001 to 2009 and the BSSS and non-BSSS inbreds had genotypic data for 669 single nucleotide polymorphism (SNP) markers. Single-cross performance was predicted by a previous best linear unbiased prediction (BLUP) approach that utilized marker-based relatedness and information on relatives, and from genomewide marker effects calculated by ridge-regression BLUP (RR-BLUP). With BLUP, the mean prediction accuracy (r _MG) of single-cross performance was 0.87 for grain yield, 0.90 for grain moisture, 0.69 for stalk lodging, and 0.84 for root lodging. The BLUP and RR-BLUP models did not lead to r _MG values that differed significantly. We then used the RR-BLUP model, developed from single-cross data, to predict the performance of testcrosses within 14 biparental populations. The r _MG values within each testcross population were generally low and were often negative. These results were obtained despite the above-average level of linkage disequilibrium, i.e., r ² between adjacent markers of 0.35 in the BSSS inbreds and 0.26 in the non-BSSS inbreds. Overall, our results suggested that genomewide marker effects estimated from maize single crosses are not advantageous (compared with BLUP) for predicting single-cross performance and have erratic usefulness for predicting testcross performance within a biparental cross.     

Computer comparison of new and existing criteria for constructing evolutionary trees from sequence data

Summary Three new methods for constructing evolutionary trees from molecular sequence data are presented. These methods are based on a theory for correcting for non-constant evolutionary rates (Klotz et al. 1979; Klotz and Blanken 1981). Extensive computer simulations were run to compare these new methods to the commonly used criteria of Dayhoff (1978) and Fitch and Margoliash (1967). The results of these simulations showed that two of the new methods performed as well as Dayhoff's criterion, significantly better than that of Fitch and Margoliash, and as well as a simple variation of the latter (Prager and Wilson 1978) where any topology containing negative branch mutations is discarded. However, no method yielded the correct topology all of the time, which demonstrated the need to determine confidence estimates in a particular result when evolutionary trees are determined from sequence data.     

Some bold evolutionary predictions for the future of mating in humans

Why are many human populations presently ‘imploding’ with below‐replacement fertility? Why are more and more young adults in these societies choosing to remain single and/or childless? Based on first principles of evolutionary theory, predictions can be derived for changes over time in the relative frequency distributions of four traits in humans proposed as the most direct determinants of the propensity to mate and reproduce: attractions to sex, legacy, leisure and parenting. In the past, high fitness was most profoundly determined by strong sex drive and strong legacy drive, especially in males. Female fertility was largely controlled by dominant males, who were then free to engage in attractions to both leisure and legacy through ‘memes’ (as well as through genes, or offspring) without any penalty on fitness. Natural selection in the past, therefore, neither strongly favoured nor strongly disfavoured any particular intrinsic female inclinations or preferences that might affect offspring production. The recent, widespread, and continuing rise in the empowerment of women, however, defines a dramatically different contemporary selection regime, where women are now free to indulge in their evolved attractions to leisure and legacy through memes inherited from predecessors, both of which represent compelling distractions from parenthood. The implications for the future survival of marriage and parenthood as cultural institutions look dismal in the short term, but promising in the long term.     

Haploid evolutionary constructor: new features and further challenges

In this paper we consider the recent advances in methodology for modeling of prokaryotic communities evolution and new features of the software package "Haploid evolutionary constructor" (http://evol-constructor.bionet.nsc.ru). We show the principles of building complex computer models in our software tool. These models describe several levels of biological organization: genetic, metabolic, population, ecological. New features of the haploid evolutionary constructor include the modeling of gene networks and phage infections.     

MultiSeq: unifying sequence and structure data for evolutionary analysis

Background  

Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes.     

Drag reduction in wave-swept macroalgae: Alternative strategies and new predictions

? Premise of the study: Intertidal macroalgae must resist extreme hydrodynamic forces imposed by crashing waves. How does frond flexibility mitigate drag, and how does flexibility affect predictions of drag and dislodgement in the field? ? Methods: We characterized flexible reconfiguration of six seaweed species in a recirculating water flume, documenting both shape change and area reduction as fronds reorient. We then used a high-speed gravity-accelerated water flume to test our ability to predict drag under waves based on extrapolations of drag recorded at slower speeds. We compared dislodgement forces to drag forces predicted from slow- and high-speed data to generate new predictions of survivorship and maximum sustainable frond size along wave-swept shores. ? Key results: Bladed algae were generally "shape changers", limiting drag by reducing drag coefficients, whereas the branched alga Calliarthron was an "area reducer", limiting drag by reducing projected area in flow. Drag predictions often underestimated actual drag measurements at high speeds, suggesting that slow-speed data may not reflect the performance of flexible seaweeds under breaking waves. Several seaweeds were predicted to dislodge at similar combinations of velocity and frond size, suggesting common scaling factors of dislodgement strength and drag. ? Conclusions: Changing shape and reducing projected area in flow are two distinct strategies employed by flexible seaweeds to resist drag. Flexible reconfiguration contributes to the uncertainty of drag extrapolation, and researchers should use caution when predicting drag and dislodgement of seaweeds in the field.