Understanding Evolutionary Trees

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

Diversity of Mechanical Architectures in Climbing Plants: An Evolutionary Perspective

Mechanical architectures of a wide range of climbing plants are reviewed from a wide phylogenetic range and evolutionary contingencies. They include an herbaceous lycopod (Lycopodiaceae) - a woody tropical liana (Apocynaceae), temperate climbers, herbs and shrubs (Ranunculacae), and two representative climbing palms (Arecoideae, Calamoideae). Trends in mechanical properties during development are reviewed and interpreted via changes in anatomical development of the stem and type of connection to host supports. The results indicate that there are some biomechanical features common to diverse climbing plants including (1) phases of relatively rigid stem growth where the climbing stem has to span between supports and (2) a mechanism to achieve greater compliancy towards the base or at points where the slender climbing stem is at risk from excessive mechanical stress. Evolutionary contingencies such as basal plesiomorphic constraint, complexification, simplification and developmental loss can drastically influence ways in which different plants have evolved different biomechanical climbing architectures. Two key developmental features controlling the biomechanics of the climbing stem are (1) the presence/absence of secondary growth and (2) the number, complexity and coordination of development of primary or secondary tissues with varying mechanical properties. Recent research has suggested that evolution of specialized climbing architectures can canalize subsequent evolution of alternative growth forms. The results suggest that the origin and type of climbing architecture can be heavily influenced by ancestral growth forms and architectures. Despite the extremely complex patterns of plant growth form evolution involving escapes to and from more specialized or simpler bauplans, selective pressure towards non-self-supporting growth forms is a remarkably persistent and iterative feature of growth form evolution in land plants.     

The Evolutionary Potential of Phenotypic Mutations

Errors in protein synthesis, so-called phenotypic mutations, are orders-of-magnitude more frequent than genetic mutations. Here, we provide direct evidence that alternative protein forms and phenotypic variability derived from translational errors paved the path to genetic, evolutionary adaptations via gene duplication. We explored the evolutionary origins of Saccharomyces cerevisiae IDP3 - an NADP-dependent isocitrate dehydrogenase mediating fatty acids ß-oxidation in the peroxisome. Following the yeast whole genome duplication, IDP3 diverged from a cytosolic ancestral gene by acquisition of a C-terminal peroxisomal targeting signal. We discovered that the pre-duplicated cytosolic IDPs are partially localized to the peroxisome owing to +1 translational frameshifts that bypass the stop codon and unveil cryptic peroxisomal targeting signals within the 3’-UTR. Exploring putative cryptic signals in all 3’-UTRs of yeast genomes, we found that other enzymes related to NADPH production such as pyruvate carboxylase 1 (PYC1) might be prone to peroxisomal localization via cryptic signals. Using laboratory evolution we found that these translational frameshifts are rapidly imprinted via genetic single base deletions occurring within the very same gene location. Further, as exemplified here, the sequences that promote translational frameshifts are also more prone to genetic deletions. Thus, genotypes conferring higher phenotypic variability not only meet immediate challenges by unveiling cryptic 3’-UTR sequences, but also boost the potential for future genetic adaptations.     

Potential Germline Competition in Animals and Its Evolutionary Implications

Mutation, mitotic crossing over and mitotic gene conversion can create genetic diversity in otherwise uniform diploid cell lineages. In the germline this diversification may result in competition between diploid germline phenotypes, with subsequent biases in the frequency of alleles transmitted to the offspring. Sperm competition is a well documented feature of many higher organisms and a model is developed to quantify this process. Competition, and hence selection, can also occur by differential survival of diploid lineages before meiosis. It is concluded that under certain circumstances germline selection is an efficient means of eliminating unfavorable alleles from the population. This does not require differences in adult fertility or viability which is the usual mechanism cited as causing changes in gene frequency in a population. It is proposed that such competition may play a role in maintaining the efficiency of basic metabolic pathways.     

Understanding Current and Potential Consequences of Population Growth

In three semiguided inquiry lessons on population biology, students use models and simulations to examine population trends and make projections. They are guided to create and evaluate data and to use algebraic and geometric representations to examine biotic and logistic growth models as part of examining human population growth. As they recognize the relationship between population growth and resources, they explore and propose solutions for addressing complex socioscientific problems. The underlying mathematics and science concepts of these learning cycle lessons can help students understand the complexity of environmental issues and prepare them to reason in an informed manner when they encounter debates on population and environmental issues that are often voiced in political arenas.     

Properties and Evolutionary Potential of Newly Induced Tandem Duplications in DROSOPHILA MELANOGASTER

Most of some 33 X-ray-induced duplications recovered as Suppressors of Minute loci proved to be direct tandem duplications. When heterozygous, most duplications were crossover suppressors, and duplications of short to moderate size did not reduce the fitness of their bearers. Crossover suppression by tandem duplication may be attributed to intrastrand foldbacks of the type regularly seen in somatic polytene chromosomes. As a consequence, linkage disequilibrium between duplicated elements and normal chromosomes should be more profound than has been supposed. Tandem duplications appear to be predisposed by reason of frequency of generation, crossover suppression and fitness effects to serve as the primary source of new genes.     

Emergence and Transmission of Arbovirus Evolutionary Intermediates with Epidemic Potential

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Understanding and Enhancing the Role of the Mass Media in Evolutionary Psychology Education

Mass media has always been a prominent source of science information for the general public, and more so than academic journals. The diversification of media with specialized online outlets and the participatory nature of the Internet have opened opportunities, as well as challenges, for researchers and educators. This paper represents our attempt to address this issue with respect to human evolutionary behavioral sciences, and suggest ways to successfully navigate interactions with the mass media for effective evolutionary education. We briefly review how one can interact with the mass media for educational purposes, focusing on how best to situate one’s research within evolutionary theory. We describe our own experiences and those of other academic colleagues who have received mass media attention, noting both positive and negative results. We also provide specific tips on how to best interact with various forms of media.     

Towards an Evolutionary Understanding of Questing Behaviour in the Tick Ixodes ricinus

The tick Ixodes ricinus finds its hosts by climbing vegetation and adopting a sit-and-wait tactic. This “questing” behaviour is known to be temperature-dependent, such that questing increases with temperature up to a point where the vapor pressure deficit (drying effect) forces ticks down to rehydrate in the soil or mat layer. Little if any attention has been paid to understanding the questing of ticks from an evolutionary perspective. Here we ask whether populations from colder climatic conditions respond differently in terms of the threshold temperature for questing and the rate of response to a fixed temperature. We find significant variation between populations in the temperature sensitivity of questing, with populations from cooler climates starting questing at lower temperatures than populations from warmer temperatures. Cool climate populations also quest sooner when the temperature is held constant. These patterns are consistent with local adaptation to temperature either through direct selection or acclimation and challenge the use of fixed thresholds for questing in modeling the spread of tick populations. Our results also show how both time and temperature play a role in questing, but we are unable to explain the relationship in terms of degree-time used to model Arthropod development. We find that questing in response to temperature fits well with a quantitative genetic model of the conditional strategy, which reveals how selection on questing may operate and hence may be of value in understanding the evolutionary ecology of questing.     

Amphibian Anomalies as a Source of Information on the Adaptive and Evolutionary Potential

Long-term data on the morphological anomalies of four anuran species (family Ranidae) and two tailed amphibian species (families Hynobiidae and Salamandridae), inhabiting forest and urbanized areas in the eastern slope of the Middle Urals, have been studied. The morphological deviations of amphibians were investigated in terms of the module principle, which predetermines the similarity of evolutionary transformations in different taxa and limit the number of possible directions of diversification in morphogenesis. The definitive spectra and frequencies of morphological anomalies in juvenile and adult individuals are compared in the urbanization gradient. Original methodological and methodical approaches to using the potential and implemented spectra of deviation are proposed for assessing the role of the ecological component in their formation. The possibility of using deviant forms of variability for assessing the evolutionary and adaptive potentials of the species is discussed.     

“Virtual Inquiry”: Teaching Molecular Aspects of Evolutionary Biology Through Computer-Based Inquiry

Genetic diversity is a core concept in evolutionary biology; genetic variation is a prerequisite for heritable differential selection, and biodiversity plays a central role in debates about environmental policy today. The technique of gel electrophoresis provides a simple, visual demonstration of the variation that exists on the genetic level among individuals of a species. “DNA fingerprinting”, in particular, is a method that exploits variation within species and has been explored extensively by the news media and popular television shows. In this paper, we suggest that science educators can capitalize on this momentum of interest and incorporate gel electrophoresis to their teaching as a starting point for the examination of genetic diversity that connects fundamental concepts of the molecular, cellular, organismic, and population levels of ecological organization. As a pedagogical tool toward this aim, we examine how increasingly complex inquiry learning can be supported in classrooms by the application of software tools called “virtual laboratories”. The paper is a synthesis of current research on the integration of software design and instructional design to illustrate how two software tools can be employed for different levels of inquiry learning.     

Genome Structure and Reproductive Behaviour Influence the Evolutionary Potential of a Fungal Phytopathogen

Modern agriculture favours the selection and spread of novel plant diseases. Furthermore, crop genetic resistance against pathogens is often rendered ineffective within a few years of its commercial deployment. Leptosphaeria maculans, the cause of phoma stem canker of oilseed rape, develops gene-for-gene interactions with its host plant, and has a high evolutionary potential to render ineffective novel sources of resistance in crops. Here, we established a four-year field experiment to monitor the evolution of populations confronted with the newly released Rlm7 resistance and to investigate the nature of the mutations responsible for virulence against Rlm7. A total of 2551 fungal isolates were collected from experimental crops of a Rlm7 cultivar or a cultivar without Rlm7. All isolates were phenotyped for virulence and a subset was genotyped with neutral genetic markers. Virulent isolates were investigated for molecular events at the AvrLm4-7 locus. Whilst virulent isolates were not found in neighbouring crops, their frequency had reached 36% in the experimental field after four years. An extreme diversity of independent molecular events leading to virulence was identified in populations, with large-scale Repeat Induced Point mutations or complete deletion of AvrLm4-7 being the most frequent. Our data suggest that increased mutability of fungal genes involved in the interactions with plants is directly related to their genomic environment and reproductive system. Thus, rapid allelic diversification of avirulence genes can be generated in L. maculans populations in a single field provided that large population sizes and sexual reproduction are favoured by agricultural practices.     

Modeling the Evolutionary Architectures of Transcribed Human Enhancer Sequences Reveals Distinct Origins,Functions, and Associations with Human Trait Variation

Despite the importance of gene regulatory enhancers in human biology and evolution, we lack a comprehensive model of enhancer evolution and function. This substantially limits our understanding of the genetic basis of species divergence and our ability to interpret the effects of noncoding variants on human traits.To explore enhancer sequence evolution and its relationship to regulatory function, we traced the evolutionary origins of transcribed human enhancer sequences with activity across diverse tissues and cellular contexts from the FANTOM5 consortium. The transcribed enhancers are enriched for sequences of a single evolutionary age (“simple” evolutionary architectures) compared with enhancers that are composites of sequences of multiple evolutionary ages (“complex” evolutionary architectures), likely indicating constraint against genomic rearrangements. Complex enhancers are older, more pleiotropic, and more active across species than simple enhancers. Genetic variants within complex enhancers are also less likely to associate with human traits and biochemical activity. Transposable-element-derived sequences (TEDS) have made diverse contributions to enhancers of both architectures; the majority of TEDS are found in enhancers with simple architectures, while a minority have remodeled older sequences to create complex architectures. Finally, we compare the evolutionary architectures of transcribed enhancers with histone-mark-defined enhancers.Our results reveal that most human transcribed enhancers are ancient sequences of a single age, and thus the evolution of most human enhancers was not driven by increases in evolutionary complexity over time. Our analyses further suggest that considering enhancer evolutionary histories provides context that can aid interpretation of the effects of variants on enhancer function. Based on these results, we propose a framework for analyzing enhancer evolutionary architecture.     

Evolution of Bow-Tie Architectures in Biology

Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.     

Understanding the Potential Impact of a Combination HIV Prevention Intervention in a Hyper-Endemic Community

Objectives

Despite demonstrating only partial efficacy in preventing new infections, available HIV prevention interventions could offer a powerful strategy when combined. In anticipation of combination HIV prevention programs and research studies we estimated the population-level impact of combining effective scalable interventions at high population coverage, determined the factors that influence this impact, and estimated the synergy between the components.

Methods

We used a mathematical model to investigate the effect on HIV incidence of a combination HIV prevention intervention comprised of high coverage of HIV testing and counselling, risk reduction following HIV diagnosis, male circumcision for HIV-uninfected men, and antiretroviral therapy (ART) for HIV-infected persons. The model was calibrated to data for KwaZulu-Natal, South Africa, where adult HIV prevalence is approximately 23%.

Results

Compared to current levels of HIV testing, circumcision, and ART, the combined intervention with ART initiation according to current guidelines could reduce HIV incidence by 47%, from 2.3 new infections per 100 person-years (pyar) to 1.2 per 100 pyar within 4 years and by almost 60%, to 1 per 100 pyar, after 25 years. Short-term impact is driven primarily by uptake of testing and reductions in risk behaviour following testing while long-term effects are driven by periodic HIV testing and retention in ART programs. If the combination prevention program incorporated HIV treatment upon diagnosis, incidence could be reduced by 63% after 4 years and by 76% (to about 0.5 per 100 pyar) after 15 years. The full impact of the combination interventions accrues over 10–15 years. Synergy is demonstrated between the intervention components.

Conclusion

High coverage combination of evidence-based strategies could generate substantial reductions in population HIV incidence in an African generalized HIV epidemic setting. The full impact could be underestimated by the short assessment duration of typical evaluations.