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1.
Background
Evolution is everywhere in Galápagos, especially regarding the role the islands have played in the history of evolutionary thought. In turn, the Galápagos National Park guides are in a unique position as informal science educators, as they are the primary points-of-contact for the islands’ ~ 200,000 tourists per year. Our goal was to assess the guides’ knowledge and acceptance of the theory of evolution, in addition to learning more about their perceptions of the connection between the islands and evolution.Methods
We surveyed 63 guides in three towns on three of the archipelago’s populated islands. Surveys included items targeting the guides knowledge of evolution (via the Knowledge of Evolution Exam, or the KEE) and acceptance of the theory of evolution (via the Measure of Acceptance of the Theory of Evolution, or the MATE). Additional, novel items gauged the guides’ perceptions of the islands, insofar as Galápagos is connected to evolution and the history of evolutionary thought.Results
Although acceptance of evolution was high, knowledge was relatively low. However, the guides are proud of the islands’ association with the history of evolutionary thought, and enjoy talking about evolution while giving tours. On open-ended responses, guides claimed to especially enjoy talking with tourists about geology and island culture, and a few voiced concerns about the conflict between evolution and religion. Finally, the overwhelming majority of the guides agreed or strongly agreed with the statement, “I would like to learn more about Galápagos and the history of evolutionary thought.”Conclusions
Galápagos guides display a disconnect between what is felt about evolution, and what is known about how evolution actually works. We can probably trace their fondness for, and acceptance of, evolution to the clear connection between evolution, tourism, and the guides’ livelihoods. We can trace their lack of knowledge to their schooling, as prior work detected similarly low knowledge of evolution in the islands’ schoolteachers. However, the guides are a receptive audience for professional development pertaining to our contemporary understanding of the mechanics of biological evolution. Improving guides’ understanding of biological evolution could, in turn, inform the evolutionary understanding of thousands of tourists each year.2.
Background
Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task.Results
We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs). We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes) of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains). We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain) are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA) of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties indicates that, even with a gain penalty of 1 (equal weights assigned to a gain and a loss), the set of 572 genes assigned to LUCA might be nearly sufficient to sustain a functioning organism. Under this gain penalty value, the numbers of horizontal gene transfer and gene loss events are nearly identical. This result holds true for two alternative topologies of the species tree and even under random shuffling of the tree. Therefore, the results seem to be compatible with approximately equal likelihoods of HGT and gene loss in the evolution of prokaryotes.Conclusions
The notion that gene loss and HGT are major aspects of prokaryotic evolution was supported by quantitative analysis of the mapping of the phyletic patterns of COGs onto a hypothetical species tree. Algorithms were developed for constructing parsimonious evolutionary scenarios, which include gene loss and gain events, for orthologous gene sets, given a species tree. This analysis shows, contrary to expectations, that the number of predicted HGT events that occurred during the evolution of prokaryotes might be approximately the same as the number of gene losses. The approach to the reconstruction of evolutionary scenarios employed here is conservative with regard to the detection of HGT because only patterns of gene presence-absence in sequenced genomes are taken into account. In reality, horizontal transfer might have contributed to the evolution of many other genes also, which makes it a dominant force in prokaryotic evolution.3.
Background
Phylogenetic networks are leaf-labeled graphs used to model and display complex evolutionary relationships that do not fit a single tree. There are two classes of phylogenetic networks: Data-display networks and evolutionary networks. While data-display networks are very commonly used to explore data, they are not amenable to incorporating probabilistic models of gene and genome evolution. Evolutionary networks, on the other hand, can accommodate such probabilistic models, but they are not commonly used for exploration.Results
In this work, we show how to turn evolutionary networks into a tool for statistical exploration of phylogenetic hypotheses via a novel application of Gibbs sampling. We demonstrate the utility of our work on two recently available genomic data sets, one from a group of mosquitos and the other from a group of modern birds. We demonstrate that our method allows the use of evolutionary networks not only for explicit modeling of reticulate evolutionary histories, but also for exploring conflicting treelike hypotheses. We further demonstrate the performance of the method on simulated data sets, where the true evolutionary histories are known.Conclusion
We introduce an approach to explore phylogenetic hypotheses over evolutionary phylogenetic networks using Gibbs sampling. The hypotheses could involve reticulate and non-reticulate evolutionary processes simultaneously as we illustrate on mosquito and modern bird genomic data sets.4.
Background
Faculty perception of student knowledge and acceptance of subject matter affects the choice of what to teach and how to teach it. Accurate assessment of student acceptance of evolution, then, is relevant to how the subject should be taught. To explore the accuracy of such assessment, we compared how community college instructors of life sciences courses perceive students’ attitudes towards evolution with those students’ actual attitudes towards evolution.Results
The research had two components: (1) a survey of students of several biology classes at a community college about their acceptance of evolutionary theory and (2) interviews with the biology faculty teaching those classes about their perceptions of their students’ attitudes towards evolution. Results of the study indicate relatively high levels of acceptance of evolution among community college students at this West Coast institution. We also found that community college instructors of life sciences courses varied in accuracy of their perceptions of their students’ attitudes towards evolution–but not systematically. Although one professor assessed each class quite accurately, the other two professors frequently underestimated the acceptance of evolution among their students.Conclusions
Errors in perception seemed independent of whether the class was composed of majors, nonmajors, or a combination. Clearly, in our sample there is much idiosyncrasy regarding community college instructor accuracy concerning student opinions about evolution.5.
Katie F. Manwaring Jamie L. Jensen Richard A. Gill Richard R. Sudweeks Randall S. Davies Seth M. Bybee 《Evolution》2018,11(1):2
Background
Acceptance of evolutionary theory varies widely and is often associated with religious background. Some have suggested there exists an additional relationship between scientific reasoning ability and the acceptance of evolutionary theory. In this study, we used structural equation modeling to test whether scientific reasoning ability predicts religiosity, acceptance of creationist views, or acceptance of evolution. We administered internet-based surveys to 724 individuals nationwide who self-describe as being religious and built a structural-equation model to test predictive abilities.Results
We found that while religiosity positively predicts the acceptance of creationist views and negatively predicts the acceptance of evolution, scientific reasoning ability does not predict religiosity, acceptance of creationist views, or acceptance of evolutionary theory.Conclusions
With a lack of any relationship between scientific reasoning ability and acceptance, an approach to evolution education that focuses on appealing to scientific reasoning may prove fruitless in changing student attitudes toward evolution; alternative teaching approaches regarding evolution are warranted.6.
M. Elizabeth Barnes E. Margaret Evans Ashley Hazel Sara E. Brownell Randolph M. Nesse 《Evolution》2017,10(1):7
Background
How acceptance of evolution relates to understanding of evolution remains controversial despite decades of research. It even remains unclear whether cultural/attitudinal factors or cognitive factors have a greater impact on student ability to learn evolutionary biology. This study examined the influence of cultural/attitudinal factors (religiosity, acceptance of evolution, and parents’ attitudes towards evolution) and cognitive factors (teleological reasoning and prior understanding of natural selection) on students’ learning of natural selection over a semester-long undergraduate course in evolutionary medicine.Method
Pre-post course surveys measured cognitive factors, including teleological reasoning and prior understanding of natural selection, and also cultural/attitudinal factors, including acceptance of evolution, parent attitudes towards evolution, and religiosity. We analyzed how these measures influenced increased understanding of natural selection over the semester.Results
After controlling for other related variables, parent attitude towards evolution and religiosity predicted students’ acceptance of evolution, but did not predict students’ learning gains of natural selection over the semester. Conversely, lower levels of teleological reasoning predicted learning gains in understanding natural selection over the course, but did not predict students’ acceptance of evolution.Conclusions
Acceptance of evolution did not predict students’ ability to learn natural selection over a semester in an evolutionary medicine course. However, teleological reasoning did impact students’ ability to learn natural selection.7.
Background
Since the reclassification of all life forms in three Domains (Archaea, Bacteria, Eukarya), the identity of their alleged forerunner (Last Universal Common Ancestor or LUCA) has been the subject of extensive controversies: progenote or already complex organism, prokaryote or protoeukaryote, thermophile or mesophile, product of a protracted progression from simple replicators to complex cells or born in the cradle of "catalytically closed" entities? We present a critical survey of the topic and suggest a scenario.Results
LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse. LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies, i.e. instances where a protein tree departs from the SSU-rRNA genealogy; consequently, horizontal gene transfer may not have the rampant character assumed by many. Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane, composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion. Bacteria emerged by reductive evolution from LUCA and some lineages further acquired extreme thermophily by convergent evolution. This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from different viral invasions as proposed by Forterre. Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's ancestors having emerged as complex, self-replicating entities from which a genetic code arose under natural selection.Conclusion
Life was born complex and the LUCA displayed that heritage. It had the "body "of a mesophilic eukaryote well before maturing by endosymbiosis into an organism adapted to an atmosphere rich in oxygen. Abundant indications suggest reductive evolution of this complex and heterogeneous entity towards the "prokaryotic" Domains Archaea and Bacteria. The word "prokaryote" should be abandoned because epistemologically unsound.Reviewers
This article was reviewed by Anthony Poole, Patrick Forterre, and Nicolas Galtier.8.
Background
DNA replication requires contributions from various proteins, such as DNA helicases; in mitochondria Twinkle is important for maintaining and replicating mitochondrial DNA. Twinkle helicases are predicted to also possess primase activity, as has been shown in plants; however this activity appears to have been lost in metazoans. Given this, the study of Twinkle in other organisms is required to better understand the evolution of this family and the roles it performs within mitochondria.Results
Here we describe the characterization of a Twinkle homologue, Twm1, in the amoeba Dictyostelium discoideum, a model organism for mitochondrial genetics and disease. We show that Twm1 is important for mitochondrial function as it maintains mitochondrial DNA copy number in vivo. Twm1 is a helicase which unwinds DNA resembling open forks, although it can act upon substrates with a single 3′ overhang, albeit less efficiently. Furthermore, unlike human Twinkle, Twm1 has primase activity in vitro. Finally, using a novel in bacterio approach, we demonstrated that Twm1 promotes DNA replication.Conclusions
We conclude that Twm1 is a replicative mitochondrial DNA helicase which is capable of priming DNA for replication. Our results also suggest that non-metazoan Twinkle could function in the initiation of mitochondrial DNA replication. While further work is required, this study has illuminated several alternative processes of mitochondrial DNA maintenance which might also be performed by the Twinkle family of helicases.9.
Marc Hellmuth 《Algorithms for molecular biology : AMB》2017,12(1):23
Background
The history of gene families—which are equivalent to event-labeled gene trees—can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are biologically feasible, that is, if there is a possible true history that would explain a given gene tree. In practice, this problem is boiled down to finding a reconciliation map—also known as DTL-scenario—between the event-labeled gene trees and a (possibly unknown) species tree.Results
In this contribution, we first characterize whether there is a valid reconciliation map for binary event-labeled gene trees T that contain speciation, duplication and horizontal gene transfer events and some unknown species tree S in terms of “informative” triples that are displayed in T and provide information of the topology of S. These informative triples are used to infer the unknown species tree S for T. We obtain a similar result for non-binary gene trees. To this end, however, the reconciliation map needs to be further restricted. We provide a polynomial-time algorithm to decide whether there is a species tree for a given event-labeled gene tree, and in the positive case, to construct the species tree and the respective (restricted) reconciliation map. However, informative triples as well as DTL-scenarios have their limitations when they are used to explain the biological feasibility of gene trees. While reconciliation maps imply biological feasibility, we show that the converse is not true in general. Moreover, we show that informative triples neither provide enough information to characterize “relaxed” DTL-scenarios nor non-restricted reconciliation maps for non-binary biologically feasible gene trees.10.
Background
Maximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs. Since the problem of finding temporally feasible maximum parsimony reconciliations is NP-complete, current methods use either exact algorithms with exponential worst-case running time or heuristics that do not guarantee optimal solutions.Results
We offer an efficient new approach that begins with a potentially infeasible maximum parsimony reconciliation and iteratively “repairs” it until it becomes temporally feasible.Conclusions
In a non-trivial number of cases, this approach finds solutions that are better than those found by the widely-used Jane heuristic.11.
Background
The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding the mapping that minimizes the number of duplication and loss events. Probabilistic modeling of gene duplication and loss is relatively new and has largely focused on birth-death processes.Results
We introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths. We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model. We implemented the algorithm in the program DrML and verified its performance with empirical and simulated data.Conclusions
In test data sets, DrML finds optimal gene duplication and loss scenarios within minutes, even when the gene trees contain sequences from several hundred species. In many cases, these optimal scenarios differ from the lca-mapping that results from a parsimony gene tree reconciliation. Thus, DrML provides a new, practical statistical framework on which to study gene duplication.12.
13.
Background
The facial musculature is a remarkable anatomical complex involved in vital activities of fishes, such as food capture and gill ventilation. The evolution of the facial muscles is largely unknown in most major fish lineages, such as the Actinopterygii. This megadiverse group includes all ray-finned fishes and comprises approximately half of the living vertebrate species. The Polypteriformes, Acipenseriformes, Lepisosteiformes, Amiiformes, Elopiformes, and Hiodontiformes occupy basal positions in the actinopterygian phylogeny and a comparative study of their facial musculature is crucial for understanding the cranial evolution of bony fishes (Osteichthyes) as a whole.Results
The facial musculature of basal actinopterygians is revised, redescribed, and analyzed under an evolutionary perspective. We identified twenty main muscle components ontogenetically and evolutionarily derived from three primordial muscles. Homologies of these components are clarified and serve as basis for the proposition of a standardized and unifying myological terminology for all ray-finned fishes. The evolutionary changes in the facial musculature are optimized on the osteichthyan tree and several new synapomorphies are identified for its largest clades, including the Actinopterygii, Neopterygii, and Teleostei. Myological data alone ambiguously support the monophyly of the Holostei. A newly identified specialization constitutes the first unequivocal morphological synapomorphy for the Elopiformes. The myological survey additionally allowed a reinterpretation of the homologies of ossifications in the upper jaw of acipenseriforms.Conclusions
The facial musculature proved to be extremely informative for the higher-level phylogeny of bony fishes. These muscles have undergone remarkable changes during the early radiation of ray-finned fishes, with significant implications for the knowledge of the musculoskeletal evolution of both derived actinopterygians and lobe-finned fishes (Sarcopterygii).14.
Background
Despite decades of education reform efforts, the percent of the general US population accepting biological evolution as the explanation for the diversity of life has remained relatively unchanged over the past 35 years. Previous work has shown the importance of both educational and non-educational (sociodemographic and psychological) factors on acceptance of evolution, but has often looked at such factors in isolation. Our study is among the first attempts to model quantitatively how the unique influences of evolutionary content knowledge, religiosity, epistemological sophistication, and an understanding of the nature of science collectively predict an individual’s acceptance or rejection of evolution.Results
Our study population had a high acceptance of evolution, with an average score of 77.17 (95% C.I. ± 1.483) on the Measure of Acceptance of the Theory of Evolution (MATE) instrument. Our combined general linear model showed that, of the variables in our model, an understanding of the nature of science explained the greatest amount of variation in acceptance of evolution. This was followed in amount of variance explained by a measure of religiosity, openness to experience, religious denomination, number of biology courses previously taken, and knowledge of evolutionary biology terms.Conclusions
Understanding of the nature of science was the single most important factor associated with acceptance of evolution in our study and explained at least four times more variation than measures of evolutionary knowledge. This suggests that educational efforts to impact evolutionary acceptance should focus on increasing an understanding of the nature of science (which may be expected to have additional benefits towards generalized science denial). Additionally, our measure of epistemological sophistication had a unique, significant impact on acceptance of evolution. Both epistemological sophistication and an understanding of the nature of science are factors that might change throughout a liberal arts education, independent of the effect of direct evolutionary instruction.15.
Background
As predicted by theory, traits associated with reproduction often evolve at a comparatively high speed. This is especially the case for courtship behaviour which plays a central role in reproductive isolation. On the other hand, courtship behavioural traits often involve morphological and behavioural adaptations in both sexes; this suggests that their evolution might be under severe constraints, for instance irreversibility of character loss. Here, we use a recently proposed method to retrieve data on a peculiar courtship behavioural trait, i.e. antennal coiling, for 56 species of diplazontine parasitoid wasps. On the basis of a well-resolved phylogeny, we reconstruct the evolutionary history of antennal coiling and associated morphological modifications to study the mode of evolution of this complex character system.Results
Our study reveals a large variation in shape, location and ultra-structure of male-specific modifications on the antennae. As for antennal coiling, we find either single-coiling, double-coiling or the absence of coiling; each state is present in multiple genera. Using a model comparison approach, we show that the possession of antennal modifications is highly correlated with antennal coiling behaviour. Ancestral state reconstruction shows that both antennal modifications and antennal coiling are highly congruent with the molecular phylogeny, implying low levels of homoplasy and a comparatively low speed of evolution. Antennal coiling is lost on two independent occasions, and never reacquired. A zero rate of regaining antennal coiling is supported by maximum parsimony, maximum likelihood and Bayesian approaches.Conclusions
Our study provides the first comparative evidence for a tight correlation between male-specific antennal modifications and the use of the antennae during courtship. Antennal coiling in Diplazontinae evolved at a comparatively low rate, and was never reacquired in any of the studied taxa. This suggests that the loss of antennal coiling is irreversible on the timescale examined here, and therefore that evolutionary constraints have greatly influenced the evolution of antennal courtship in this group of parasitoid wasps. Further studies are needed to ascertain whether the loss of antennal coiling is irreversible on larger timescales, and whether evolutionary constraints have influenced courtship behavioural traits in a similar way in other groups.16.
17.
Background
The work is part of a wider research project wherein we are trying to further explore the conceptual ecology of evolutionary theory of present and prospective teachers in Greece.Methods
Quantitative and qualitative research was applied. In the former a questionnaire was answered by 318 secondary school teachers who teach biology. We further interviewed eight of the teachers by means of semi structured interviews and analyzed the interviews using the QSR nVivo program.Results
Acceptance of evolution levels was found moderate both in the total cohort and among science teachers; on the one hand, this was correlated with the prevalence of low level of knowledge and understanding due to lack of previous instruction; on the other hand, their type of religiosity was not a serious obstacle to accepting evolution, since it was correlated with a high degree of thinking dispositions.Conclusions
The results are in agreement with our previous findings that the type of religiosity is crucial for the acceptance or rejection of evolution, particularly when it does not prevent someone from being “open-minded”. At the same time, the fact that geologists who teach science showed the highest level of acceptance of evolution, indicates, when paired with other evidence, that the geological data are the most convincing evidence to help students and teachers to make a first step in their multistep route towards accepting and understanding the theory of evolution.18.
Geoffrey A. Mueller Peter M. Thompson Eugene F. DeRose Thomas M. O’Connell Robert E. London 《Metabolomics : Official journal of the Metabolomic Society》2016,12(12):187
Background
Studies on ragweed and birch pollen extracts suggested that the adenosine content is an important factor in allergic sensitization. However, exposure levels from other pollens and considerations of geographic and seasonal factors have not been evaluated.Objective
This study compared the metabolite profile of pollen species important for allergic disease, specifically measured the adenosine content, and evaluated exposure to pollen-derived adenosine.Methods
An NMR metabolomics approach was used to measure metabolite concentrations in 26 pollen extracts. Pollen count data was analyzed from five cities to model exposure.Results
A principal component analysis of the various metabolites identified by NMR showed that pollen extracts could be differentiated primarily by sugar content: glucose, fructose, sucrose, and myo-inositol. In extracts of 10 mg of pollen/ml, the adenosine was highest for grasses (45 µM) followed by trees (23 µM) and weeds (19 µM). Pollen count data showed that tree pollen was typically 5–10 times the amount of other pollens. At the daily peaks of tree, grass, and weed season the pollen-derived adenosine exposure per day is likely to be only 1.1, 0.11, and 0.12 µg, respectively. Seasonal models of pollen exposure and respiration suggest that it would be a rare event limited to tree pollen season for concentrations of pollen-derived adenosine to approach physiological levels.Conclusion
Sugar content and other metabolites may be useful in classifying pollens. Unless other factors create localized exposures that are very different from these models, pollen-derived adenosine is unlikely to be a major factor in allergic sensitization.19.
Background
Recent coevolutionary analysis has considered tree topology as a means to reduce the asymptotic complexity associated with inferring the complex coevolutionary interrelationships that arise between phylogenetic trees. Targeted algorithmic design for specific tree topologies has to date been highly successful, with one recent formulation providing a logarithmic space complexity reduction for the dated tree reconciliation problem.Methods
In this work we build on this prior analysis providing a further asymptotic space reduction, by providing a new formulation for the dynamic programming table used by a number of popular coevolutionary analysis techniques. This model gives rise to a sub quadratic running time solution for the dated tree reconciliation problem for selected tree topologies, and is shown to be, in practice, the fastest method for solving the dated tree reconciliation problem for expected evolutionary trees. This result is achieved through the analysis of not only the topology of the trees considered for coevolutionary analysis, but also the underlying structure of the dynamic programming algorithms that are traditionally applied to such analysis.Conclusion
The newly inferred theoretical complexity bounds introduced herein are then validated using a combination of synthetic and biological data sets, where the proposed model is shown to provide an \(O(\sqrt{n})\) space saving, while it is observed to run in half the time compared to the fastest known algorithm for solving the dated tree reconciliation problem. What is even more significant is that the algorithm derived herein is able to guarantee the optimality of its inferred solution, something that algorithms of comparable speed have to date been unable to achieve.20.