Mitochondrial uncoupling as a regulator of life-history trajectories in birds: an experimental study in the zebra finch.

Mitochondria have a fundamental role in the transduction of energy from food into ATP. The coupling between food oxidation and ATP production is never perfect, but may nevertheless be of evolutionary significance. The 'uncoupling to survive' hypothesis suggests that 'mild' mitochondrial uncoupling evolved as a protective mechanism against the excessive production of damaging reactive oxygen species (ROS). Because resource allocation and ROS production are thought to shape animal life histories, alternative life-history trajectories might be driven by individual variation in the degree of mitochondrial uncoupling. We tested this hypothesis in a small bird species, the zebra finch (Taeniopygia guttata), by treating adults with the artificial mitochondrial uncoupler 2,4-dinitrophenol (DNP) over a 32-month period. In agreement with our expectations, the uncoupling treatment increased metabolic rate. However, we found no evidence that treated birds enjoyed lower oxidative stress levels or greater survival rates, in contrast to previous results in other taxa. In vitro experiments revealed lower sensitivity of ROS production to DNP in mitochondria isolated from skeletal muscles of zebra finch than mouse. In addition, we found significant reductions in the number of eggs laid and in the inflammatory immune response in treated birds. Altogether, our data suggest that the 'uncoupling to survive' hypothesis may not be applicable for zebra finches, presumably because of lower effects of mitochondrial uncoupling on mitochondrial ROS production in birds than in mammals. Nevertheless, mitochondrial uncoupling appeared to be a potential life-history regulator of traits such as fecundity and immunity at adulthood, even with food supplied ad libitum.

A Study of Ordered Gene Problems Featuring DNA Error Correction and DNA Fragment Assembly with a Variety of Heuristics, Genetic Algorithm Variations, and Dynamic Representations

Ordered gene problems are a very common classification of optimization problems. Because of their popularity countless algorithms have been developed in an attempt to find high quality solutions to the problems. It is also common to see many different types of problems reduced to ordered gene style problems as there are many popular heuristics and metaheuristics for them due to their popularity. Multiple ordered gene problems are studied, namely, the travelling salesman problem, bin packing problem, and graph colouring problem. In addition, two bioinformatics problems not traditionally seen as ordered gene problems are studied: DNA error correction and DNA fragment assembly. These problems are studied with multiple variations and combinations of heuristics and metaheuristics with two distinct types or representations. The majority of the algorithms are built around the Recentering- Restarting Genetic Algorithm. The algorithm variations were successful on all problems studied, and particularly for the two bioinformatics problems. For DNA Error Correction multiple cases were found with 100% of the codes being corrected. The algorithm variations were also able to beat all other state-of-the-art DNA Fragment Assemblers on 13 out of 16 benchmark problem instances.

Document Image Segmentation and Compression using Artificial Neural Networks and Evolutionary Methods

The work is intended to study the following important aspects of document image processing and develop new methods. (1) Segmentation ofdocument images using adaptive interval valued neuro-fuzzy method. (2) Improving the segmentation procedure using Simulated Annealing technique. (3) Development of optimized compression algorithms using Genetic Algorithm and parallel Genetic Algorithm (4) Feature extraction of document images (5) Development of IV fuzzy rules. This work also helps for feature extraction and foreground and background identification. The proposed work incorporates Evolutionary and hybrid methods for segmentation and compression of document images. A study of different neural networks used in image processing, the study of developments in the area of fuzzy logic etc is carried out in this work

Characterization of Histone H2A Derived Antimicrobial Peptides, Harriottins, from Sicklefin Chimaera Neoharriotta pinnata (Schnakenbeck, 1931) and Its Evolutionary Divergence with respect to CO1 and Histone H2A

Antimicrobial peptides (AMPs) are humoral innate immune components of fishes that provide protection against pathogenic infections. Histone derived antimicrobial peptides are reported to actively participate in the immune defenses of fishes. Present study deals with identification of putative antimicrobial sequences from the histone H2A of sicklefin chimaera, Neoharriotta pinnata. A 52 amino acid residue termed Harriottin-1, a 40 amino acid Harriottin-2, and a 21 mer Harriottin-3 were identified to possess antimicrobial sequence motif. Physicochemical properties andmolecular structure ofHarriottins are in agreement with the characteristic features of antimicrobial peptides, indicating its potential role in innate immunity of sicklefin chimaera. The histone H2A sequence of sicklefin chimera was found to differ from previously reported histone H2A sequences. Phylogenetic analysis based on histone H2A and cytochrome oxidase subunit-1 (CO1) gene revealed N. pinnata to occupy an intermediate position with respect to invertebrates and vertebrates

Verbal proficiency as fitness indicator: Experimental and comparative research on the evolutionary psychology of language and verbal displays

Summary: Recent research on the evolution of language and verbal displays (e.g., Miller, 1999, 2000a, 2000b, 2002) indicated that language is not only the result of natural selection but serves as a sexually-selected fitness indicator that is an adaptation showing an individual’s suitability as a reproductive mate. Thus, language could be placed within the framework of concepts such as the handicap principle (Zahavi, 1975). There are several reasons for this position: Many linguistic traits are highly heritable (Stromswold, 2001, 2005), while naturally-selected traits are only marginally heritable (Miller, 2000a); men are more prone to verbal displays than women, who in turn judge the displays (Dunbar, 1996; Locke & Bogin, 2006; Lange, in press; Miller, 2000a; Rosenberg & Tunney, 2008); verbal proficiency universally raises especially male status (Brown, 1991); many linguistic features are handicaps (Miller, 2000a) in the Zahavian sense; most literature is produced by men at reproduction-relevant age (Miller, 1999). However, neither an experimental study investigating the causal relation between verbal proficiency and attractiveness, nor a study showing a correlation between markers of literary and mating success existed. In the current studies, it was aimed to fill these gaps. In the first one, I conducted a laboratory experiment. Videos in which an actor and an actress performed verbal self-presentations were the stimuli for counter-sex participants. Content was always alike, but the videos differed on three levels of verbal proficiency. Predictions were, among others, that (1) verbal proficiency increases mate value, but that (2) this applies more to male than to female mate value due to assumed past sex-different selection pressures causing women to be very demanding in mate choice (Trivers, 1972). After running a two-factorial analysis of variance with the variables sex and verbal proficiency as factors, the first hypothesis was supported with high effect size. For the second hypothesis, there was only a trend going in the predicted direction. Furthermore, it became evident that verbal proficiency affects long-term more than short-term mate value. In the second study, verbal proficiency as a menstrual cycle-dependent mate choice criterion was investigated. Basically the same materials as in the former study were used with only marginal changes in the used questionnaire. The hypothesis was that fertile women rate high verbal proficiency in men higher than non-fertile women because of verbal proficiency being a potential indicator of “good genes”. However, no significant result could be obtained in support of the hypothesis in the current study. In the third study, the hypotheses were: (1) most literature is produced by men at reproduction-relevant age. (2) The more works of high literary quality a male writer produces, the more mates and children he has. (3) Lyricists have higher mating success than non-lyric writers because of poetic language being a larger handicap than other forms of language. (4) Writing literature increases a man’s status insofar that his offspring shows a significantly higher male-to-female sex ratio than in the general population, as the Trivers-Willard hypothesis (Trivers & Willard, 1973) applied to literature predicts. In order to test these hypotheses, two famous literary canons were chosen. Extensive biographical research was conducted on the writers’ mating successes. The first hypothesis was confirmed; the second one, controlling for life age, only for number of mates but not entirely regarding number of children. The latter finding was discussed with respect to, among others, the availability of effective contraception especially in the 20th century. The third hypothesis was not satisfactorily supported. The fourth hypothesis was partially supported. For the 20th century part of the German list, the secondary sex ratio differed with high statistical significance from the ratio assumed to be valid for a general population.

From evolution to co-evolution – An empirical study of the role of innovation, policy and public research in industrial dynamics

In the past decades since Schumpeter’s influential writings economists have pursued research to examine the role of innovation in certain industries on firm as well as on industry level. Researchers describe innovations as the main trigger of industry dynamics, while policy makers argue that research and education are directly linked to economic growth and welfare. Thus, research and education are an important objective of public policy. Firms and public research are regarded as the main actors which are relevant for the creation of new knowledge. This knowledge is finally brought to the market through innovations. What is more, policy makers support innovations. Both actors, i.e. policy makers and researchers, agree that innovation plays a central role but researchers still neglect the role that public policy plays in the field of industrial dynamics. Therefore, the main objective of this work is to learn more about the interdependencies of innovation, policy and public research in industrial dynamics. The overarching research question of this dissertation asks whether it is possible to analyze patterns of industry evolution – from evolution to co-evolution – based on empirical studies of the role of innovation, policy and public research in industrial dynamics. This work starts with a hypothesis-based investigation of traditional approaches of industrial dynamics. Namely, the testing of a basic assumption of the core models of industrial dynamics and the analysis of the evolutionary patterns – though with an industry which is driven by public policy as example. Subsequently it moves to a more explorative approach, investigating co-evolutionary processes. The underlying questions of the research include the following: Do large firms have an advantage because of their size which is attributable to cost spreading? Do firms that plan to grow have more innovations? What role does public policy play for the evolutionary patterns of an industry? Are the same evolutionary patterns observable as those described in the ILC theories? And is it possible to observe regional co-evolutionary processes of science, innovation and industry evolution? Based on two different empirical contexts – namely the laser and the photovoltaic industry – this dissertation tries to answer these questions and combines an evolutionary approach with a co-evolutionary approach. The first chapter starts with an introduction of the topic and the fields this dissertation is based on. The second chapter provides a new test of the Cohen and Klepper (1996) model of cost spreading, which explains the relationship between innovation, firm size and R&D, at the example of the photovoltaic industry in Germany. First, it is analyzed whether the cost spreading mechanism serves as an explanation for size advantages in this industry. This is related to the assumption that the incentives to invest in R&D increase with the ex-ante output. Furthermore, it is investigated whether firms that plan to grow will have more innovative activities. The results indicate that cost spreading serves as an explanation for size advantages in this industry and, furthermore, growth plans lead to higher amount of innovative activities. What is more, the role public policy plays for industry evolution is not finally analyzed in the field of industrial dynamics. In the case of Germany, the introduction of demand inducing policy instruments stimulated market and industry growth. While this policy immediately accelerated market volume, the effect on industry evolution is more ambiguous. Thus, chapter three analyzes this relationship by considering a model of industry evolution, where demand-inducing policies will be discussed as a possible trigger of development. The findings suggest that these instruments can take the same effect as a technical advance to foster the growth of an industry and its shakeout. The fourth chapter explores the regional co-evolution of firm population size, private-sector patenting and public research in the empirical context of German laser research and manufacturing over more than 40 years from the emergence of the industry to the mid-2000s. The qualitative as well as quantitative evidence is suggestive of a co-evolutionary process of mutual interdependence rather than a unidirectional effect of public research on private-sector activities. Chapter five concludes with a summary, the contribution of this work as well as the implications and an outlook of further possible research.

Human development in an evolutionary perspective

This article presents an evolutionary perspective to the study of human development. Some general assumptions for the study of development are discussed and the principal building blocks of evolutionary psychology are presented. One of them is that there is a universal human nature (which is modulate also by particular conditions of each context) and the cognitive architecture of human beings is the resulted of interactions between genes and environment. Based on those, and other assumptions, directions for the study of child development in an evolutionary stance are discussed, along with the considerations of context and development. Thus, it is assumed there is a relationship between phylogenies and ontogenetic development (the ontogenesis needs to be understood also as a product of evolution), considering the inseparability of biological, socio-cultural, cognitive emotional aspects that constitute this development. It has been concluded that the evolutionary developmental psychology has scientific relevance because it broadens our vision on human development.

Correlating Bayesian date estimates with climatic events and domestication using a bovine case study

The tribe Bovini contains a number of commercially and culturally important species, such as cattle. Understanding their evolutionary time scale is important for distinguishing between post-glacial and domestication-associated population expansions, but estimates of bovine divergence times have been hindered by a lack of reliable calibration points. We present a Bayesian phylogenetic analysis of 481 mitochondrial D-loop sequences, including 228 radiocarbon-dated ancient DNA sequences, using a multi-demographic coalescent model. By employing the radiocarbon dates as internal calibrations, we co-estimate the bovine phylogeny and divergence times in a relaxed-clock framework. The analysis yields evidence for significant population expansions in both taurine and zebu cattle, European aurochs and yak clades. The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence.

Managing threatened species – the ecological toolbox, evolutionary theory and the declining-population paradigm

1. The management of threatened species is an important practical way in which conservationists can intervene in the extinction process and reduce the loss of biodiversity. Understanding the causes of population declines (past, present and future) is pivotal to designing effective practical management. This is the declining-population paradigm identified by Caughley. 2. There are three broad classes of ecological tool used by conservationists to guide management decisions for threatened species: statistical models of habitat use, demographic models and behaviour-based models. Each of these is described here, illustrated with a case study and evaluated critically in terms of its practical application. 3. These tools are fundamentally different. Statistical models of habitat use and demographic models both use descriptions of patterns in abundance and demography, in relation to a range of factors, to inform management decisions. In contrast, behaviourbased models describe the evolutionary processes underlying these patterns, and derive such patterns from the strategies employed by individuals when competing for resources under a specific set of environmental conditions. 4. Statistical models of habitat use and demographic models have been used successfully to make management recommendations for declining populations. To do this, assumptions are made about population growth or vital rates that will apply when environmental conditions are restored, based on either past data collected under favourable environmental conditions or estimates of these parameters when the agent of decline is removed. As a result, they can only be used to make reliable quantitative predictions about future environments when a comparable environment has been experienced by the population of interest in the past. 5. Many future changes in the environment driven by management will not have been experienced by a population in the past. Under these circumstances, vital rates and their relationship with population density will change in the future in a way that is not predictable from past patterns. Reliable quantitative predictions about population-level responses then need to be based on an explicit consideration of the evolutionary processes operating at the individual level. 6. Synthesis and applications. It is argued that evolutionary theory underpins Caughley’s declining-population paradigm, and that it needs to become much more widely used within mainstream conservation biology. This will help conservationists examine critically the reliability of the tools they have traditionally used to aid management decision-making. It will also give them access to alternative tools, particularly when predictions are required for changes in the environment that have not been experienced by a population in the past.

Evolutionary history of vegetative reproduction in Porpidia s. l. (lichen-forming ascomycota)

The evolutionary history of gains and losses of vegetative reproductive propagules (soredia) in Porpidia s.l., a group of lichen-forming ascomycetes, was clarified using Bayesian Markov chain Monte Carlo (MCMC) approaches to monophyly tests and a combined MCMC and maximum likelihood approach to ancestral character state reconstructions. The MCMC framework provided confidence estimates for the reconstructions of relationships and ancestral character states, which formed the basis for tests of evolutionary hypotheses. Monophyly tests rejected all hypotheses that predicted any clustering of reproductive modes in extant taxa. In addition, a nearest-neighbor statistic could not reject the hypothesis that the vegetative reproductive mode is randomly distributed throughout the group. These results show that transitions between presence and absence of the vegetative reproductive mode within Porpidia s.l. occurred several times and independently of each other. Likelihood reconstructions of ancestral character states at selected nodes suggest that - contrary to previous thought - the ancestor to Porpidia s.l. already possessed the vegetative reproductive mode. Furthermore, transition rates are reconstructed asymmetrically with the vegetative reproductive mode being gained at a much lower rate than it is lost. A cautious note has to be added, because a simulation study showed that the ancestral character state reconstructions were highly dependent on taxon sampling. However, our central conclusions, particularly the higher rate of change from vegetative reproductive mode present to absent than vice versa within Porpidia s.l., were found to be broadly independent of taxon sampling. [Ancestral character state reconstructions; Ascomycota, Bayesian inference; hypothesis testing; likelihood; MCMC; Porpidia; reproductive systems]

A phyloclimatic study of Cyclamen

Background: The impact of global climate change on plant distribution, speciation and extinction is of current concern. Examining species climatic preferences via bioclimatic niche modelling is a key tool to study this impact. There is an established link between bioclimatic niche models and phylogenetic diversification. A next step is to examine future distribution predictions from a phylogenetic perspective. We present such a study using Cyclamen (Myrsinaceae), a group which demonstrates morphological and phenological adaptations to its seasonal Mediterranean-type climate. How will the predicted climate change affect future distribution of this popular genus of garden plants? Results: We demonstrate phylogenetic structure for some climatic characteristics, and show that most Cyclamen have distinct climatic niches, with the exception of several wide-ranging, geographically expansive, species. We reconstruct climate preferences for hypothetical ancestral Cyclamen. The ancestral Cyclamen lineage has a preference for the seasonal Mediterranean climate characteristic of dry summers and wet winters. Future bioclimatic niches, based on BIOCLIM and Maxent models, are examined with reference to a future climate scenario for the 2050s. Over the next 50 years we predict a northward shift in the area of climatic suitability, with many areas of current distribution becoming climatically unsuitable. The area of climatic suitability for every Cyclamen species is predicted to decrease. For many species, there may be no areas with a suitable climate regardless of dispersal ability, these species are considered to be at high risk of extinction. This risk is examined from a phylogenetic perspective. Conclusion: Examining bioclimatic niches from a phylogenetic perspective permits novel interpretations of these models. In particular, reconstruction of ancestral niches can provide testable hypothesis about the historical development of lineages. In the future we can expect a northwards shift in climatic suitability for the genus Cyclamen. If this proves to be the case then dispersal is the best chance of survival, which seems highly unlikely for ant-dispersed Cyclamen. Human-assisted establishment of Cyclamen species well outside their native ranges offers hope and could provide the only means of dispersal to potentially suitable future environments. Even without human intervention the phylogenetic perspective demonstrates that major lineages could survive climate change even if many species are lost.

Managing threatened species: the ecological toolbox, evolutionary theory and declining-population paradigm

1. The management of threatened species is an important practical way in which conservationists can intervene in the extinction process and reduce the loss of biodiversity. Understanding the causes of population declines (past, present and future) is pivotal to designing effective practical management. This is the declining-population paradigm identified by Caughley. 2. There are three broad classes of ecological tool used by conservationists to guide management decisions for threatened species: statistical models of habitat use, demographic models and behaviour-based models. Each of these is described here, illustrated with a case study and evaluated critically in terms of its practical application. 3. These tools are fundamentally different. Statistical models of habitat use and demographic models both use descriptions of patterns in abundance and demography, in relation to a range of factors, to inform management decisions. In contrast, behaviour-based models describe the evolutionary processes underlying these patterns, and derive such patterns from the strategies employed by individuals when competing for resources under a specific set of environmental conditions. 4. Statistical models of habitat use and demographic models have been used successfully to make management recommendations for declining populations. To do this, assumptions are made about population growth or vital rates that will apply when environmental conditions are restored, based on either past data collected under favourable environmental conditions or estimates of these parameters when the agent of decline is removed. As a result, they can only be used to make reliable quantitative predictions about future environments when a comparable environment has been experienced by the population of interest in the past. 5. Many future changes in the environment driven by management will not have been experienced by a population in the past. Under these circumstances, vital rates and their relationship with population density will change in the future in a way that is not predictable from past patterns. Reliable quantitative predictions about population-level responses then need to be based on an explicit consideration of the evolutionary processes operating at the individual level. 6. Synthesis and applications. It is argued that evolutionary theory underpins Caughley's declining-population paradigm, and that it needs to become much more widely used within mainstream conservation biology. This will help conservationists examine critically the reliability of the tools they have traditionally used to aid management decision-making. It will also give them access to alternative tools, particularly when predictions are required for changes in the environment that have not been experienced by a population in the past.

Infant Attachment Security and the Timing of Puberty: Testing an Evolutionary Hypothesis

Life-history theories of the early programming of human reproductive strategy stipulate that early rearing experience, including that reflected in infant-parent attachment security, regulates psychological, behavioral, and reproductive development. We tested the hypothesis that infant attachment insecurity, compared with infant attachment security, at the age of 15 months predicts earlier pubertal maturation. Focusing on 373 White females enrolled in the National Institute of Child Health and Human Development Study of Early Child Care and Youth Development, we gathered data from annual physical exams from the ages of 9½ years to 15½ years and from self-reported age of menarche. Results revealed that individuals who had been insecure infants initiated and completed pubertal development earlier and had an earlier age of menarche compared with individuals who had been secure infants, even after accounting for age of menarche in the infants’ mothers. These results support a conditional-adaptational view of individual differences in attachment security and raise questions about the biological mechanisms responsible for the attachment effects we discerned.

Evolutionary analysis of novel serine proteases in the venom gland transcriptome of Bitis gabonica rhinoceros

Background: Serine proteases are major components of viper venom and target various stages of the blood coagulation system in victims and prey. A better understanding of the diversity of serine proteases and other enzymes present in snake venom will help to understand how the complexity of snake venom has evolved and will aid the development of novel therapeutics for treating snake bites. Methodology and Principal Findings: Four serine protease-encoding genes from the venom gland transcriptome of Bitis gabonica rhinoceros were amplified and sequenced. Mass spectrometry suggests the four enzymes corresponding to these genes are present in the venom of B. g. rhinoceros. Two of the enzymes, rhinocerases 2 and 3 have substitutions to two of the serine protease catalytic triad residues and are thus unlikely to be catalytically active, though they may have evolved other toxic functions. The other two enzymes, rhinocerases 4 and 5, have classical serine protease catalytic triad residues and thus are likely to be catalytically active, however they have glycine rather than the more typical aspartic acid at the base of the primary specificity pocket (position 189). Based on a detailed analysis of these sequences we suggest that alternative splicing together with individual amino acid mutations may have been involved in their evolution. Changes within amino acid segments which were previously proposed to undergo accelerated change in venom serine proteases have also been observed. Conclusions and Significance: Our study provides further insight into the diversity of serine protease isoforms present within snake venom and discusses their possible functions and how they may have evolved. These multiple serine protease isoforms with different substrate specificities may enhance the envenomation effects and help the snake to adapt to new habitats and diets. Our findings have potential for helping the future development of improved therapeutics for snake bites.

Evolutionary genomics of the Fox genes: origin of gene families and the ancestry of gene clusters

Over the past decade genomic approaches have begun to revolutionise the study of animal diversity. In particular, genome sequencing programmes have spread beyond the traditional model species to encompass an increasing diversity of animals from many different phyla, as well as unicellular eukaryotes that are closely related to the animals. Whole genome sequences allow researchers to establish, with reasonable confidence, the full complement of any particular family of genes in a genome. Comparison of gene complements from appropriate genomes can reveal the evolutionary history of gene families, indicating when both gene diversification and gene loss have occurred. More than that, however, assembled genomes allow the genomic environment in which individual genes are found to be analysed and compared between species. This can reveal how gene diversification occurred. Here, we focus on the Fox genes, drawing from multiple animal genomes to develop an evolutionary framework explaining the timing and mechanism of origin of the diversity of animal Fox genes. Ancient linkages between genes are a prominent feature of the Fox genes, depicting a history of gene clusters, some of which may be relevant to understanding Fox gene function.