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We developed a sonification algorithm to communicate data on biodiversity decline. We used a method of data representation that caused emotional effects on listeners, with the aim of enhancing personal awareness of impacts of biodiversity decline to encourage listeners to affect change. To create the emotional effect, we chose to degrade familiar audio files as our mode of sonification. Our algorithm takes as input an audio file in a wave (.wav) format and a dataset: the WWF's Living Planet Index (LPI) from 1970 to 2018. The algorithm deletes soundwave data from the audio file proportional to the decline of biodiversity measured by the data. Thus, our auditory metaphor uses the progressive damage of the audio file at later timestamps to represent the environmental damage of biodiversity decline. To investigate the subjective listening experience of the sonifications, we held five focus groups with 13 participants and conducted thematic content analysis of the transcribed audio recordings. Participants listened to various instances of the algorithm using different input sound files, including vocal and instrumental music, a field recording, and spoken aloud poems. Focus groups suggested the algorithm was successful in communicating the data, with all participants acknowledging this success. Participants described experiencing vivid auditory metaphors and reported strong emotional responses, including sadness, loss, stress, anxiety, and optimism. Participants affirmed the greater presence of emotional response compared to a static graph-based visualisation of the same data. We propose that sonification through degradation of familiar audio files will have broad applicability in communication and public engagement with conservation issues. [Display omitted] • A novel sonification algorithm uses soundwave-level deletion successfully to represent biodiversity loss data. • Sonification creates a stronger emotional response than a two-dimensional static visualisation. • Using familiar sound for sonification creates strong emotional impacts. • The method has potential to promote behavioural change in response to biodiversity and other time-series data. [ABSTRACT FROM AUTHOR]

Bioinformatics is the use of computers in biology, particularly to analyse DNA and protein sequences and associated data. Bioinformatics has become crucial to most areas of life sciences research. However, bioinformatics education has not kept up with the pace of these advances. To help address this problem, we have designed an open-access bioinformatics workshop for secondary school biology pupils. The workshop is linked to the curriculum in Scotland, addressing learning objectives for Scottish Qualifications Authority Higher Biology and Human Biology. Furthermore, it aims to inspire pupils more generally and includes critical evaluation of evidence as a more generic skill. We delivered this workshop to biology pupils of seven schools in Scotland and conducted evaluations of pupil and teacher feedback. Quantitative pupil and teacher feedback suggests the workshop is useful and enjoyable, with no statistically significant difference between pupils identifying as female and pupils identifying as male. Qualitative responses suggest the workshop gives an increased knowledge of the field of bioinformatics and its importance in everyday life, and that pupils enjoy working in groups. Teachers also highlight the importance of hands-on experience in the classroom. We conclude the workshop is successful in its aims and is suitable for wider deployment. [ABSTRACT FROM AUTHOR]

Background: The use of sound to represent sequence data—sonification—has great potential as an alternative and complement to visual representation, exploiting features of human psychoacoustic intuitions to convey nuance more effectively. We have created five parameter-mapping sonification algorithms that aim to improve knowledge discovery from protein sequences and small protein multiple sequence alignments. For two of these algorithms, we investigated their effectiveness at conveying information. To do this we focussed on subjective assessments of user experience. This entailed a focus group session and survey research by questionnaire of individuals engaged in bioinformatics research. Results: For single protein sequences, the success of our sonifications for conveying features was supported by both the survey and focus group findings. For protein multiple sequence alignments, there was limited evidence that the sonifications successfully conveyed information. Additional work is required to identify effective algorithms to render multiple sequence alignment sonification useful to researchers. Feedback from both our survey and focus groups suggests future directions for sonification of multiple alignments: animated visualisation indicating the column in the multiple alignment as the sonification progresses, user control of sequence navigation, and customisation of the sound parameters. Conclusions: Sonification approaches undertaken in this work have shown some success in conveying information from protein sequence data. Feedback points out future directions to build on the sonification approaches outlined in this paper. The effectiveness assessment process implemented in this work proved useful, giving detailed feedback and key approaches for improvement based on end-user input. The uptake of similar user experience focussed effectiveness assessments could also help with other areas of bioinformatics, for example in visualisation. [ABSTRACT FROM AUTHOR]

Objective: Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results: We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education. [ABSTRACT FROM AUTHOR]

Background and Aims Genetically controlled self-incompatibility (SI) mechanisms constrain selfing and thus have contributed to the evolutionary diversity of flowering plants. In homomorphic gametophytic SI (GSI) and homomorphic sporophytic SI (SSI), genetic control is usually by the single multi-allelic locus S. Both GSI and SSI prevent self pollen tubes reaching the ovary and so are pre-zygotic in action. In contrast, in taxa with late-acting self-incompatibility (LSI), rejection is often post-zygotic, since self pollen tubes grow to the ovary, where fertilization may occur prior to floral abscission. Alternatively, lack of self fruit set could be due to early-acting inbreeding depression (EID). The aim of our study was to investigate mechanisms underlying the lack of selfed fruit set in Handroanthus heptaphyllus in order to assess the likelihood of LSI versus EID. Methods We employed four full-sib diallels to study the genetic control of LSI in H. heptaphyllus using a precociously flowering variant. We also used fluorescence microscopy to study the incidence of ovule penetration by pollen tubes in pistils that abscised following pollination or initiated fruits. Key Results All diallels showed reciprocally cross-incompatible full sibs (RCIs), reciprocally cross-compatible full sibs (RCCs) and non-reciprocally compatible full sibs (NRCs) in almost equal proportions. There was no significant difference between the incidences of ovule penetrations in abscised pistils following self- and cross-incompatible pollinations, but those in successful cross-pollinations were around 2-fold greater. Conclusions A genetic model postulating a single S locus with four S alleles, one of which, in the maternal parent, is dominant to the other three, will produce RCI, RCC and NRC full sib situations each at 33 %, consistent with our diallel results. We favour this simple genetic control over an EID explanation since none of our pollinations, successful or unsuccessful, resulted in partial embryo development, as would be expected under a whole-genome EID effect. [ABSTRACT FROM AUTHOR]

Evolution to reduce inbreeding can favor disassortative (intermorph) over assortative (intramorph) mating in hermaphroditic sexually polymorphic plant species. Heterostyly enhances disassortative pollination through reciprocal placement of stigmas and anthers of morphs and appropriate pollinators. Stylar dimorphism in which there is not reciprocal anther placement may compromise disassortative mating, particularly when there is not intramorph incompatibility. Variable rates of disassortative mating along with differential female fecundity or siring success among floral morphs could lead to variation in morph ratio. We investigated mating patterns, female fecundity, and siring success of style-length morphs in Narcissus papyraceus, a self-incompatible but morph-compatible species with dimorphic (long- and short-styled) and monomorphic (long-styled) populations in central and north regions of its range, respectively. We established experimental populations in both regions and exposed them to ambient pollinators. Using paternity analysis, we found similar siring success of morphs and high disassortative mating in most populations. Female fecundity of morphs was similar in all populations. Although these results could not completely explain the loss of dimorphism in the species' northern range, they provided evidence for the evolutionary stability of stylar dimorphism in N. papyraceus in at least some populations. Our findings support the hypothesis that prevailing intermorph mating is key for the maintenance of stylar dimorphism. [ABSTRACT FROM AUTHOR]

There is a profound need for the scientific community to be better aware of the policy context in which it operates. To address this need, Evolution has established a new Outlook feature section to include papers that explore the interface between society and evolutionary biology. This first paper in the series considers the strategic relevance of evolutionary biology. Support for scientific research in general is based on governmental or institutional expenditure that is an investment, and such investment is based on strategies designed to achieve particular outcomes, such as advance in particular areas of basic science or application. The scientific community can engage in the development of scientific strategies on a variety of levels, including workshops to explicitly develop research priorities and targeted funding initiatives to help define emerging scientific areas. Better understanding and communication of the scientific achievements of evolutionary biology, emphasizing immediate and potential societal relevance, are effective counters to challenges presented by the creationist agenda. Future papers in the Outlook feature section should assist the evolutionary biology community in achieving a better collective understanding of the societal relevance of their field. [ABSTRACT FROM AUTHOR]

The discovery that nuclear DNA content varies widely among species, and even within species, was unexpected because it was thought that the number of genes required for an organism should be common across taxa. We now know that the bulk of nuclear DNA content variation is caused by repetitive DNA sequences characterized according to the nature of repeat (tandem vs dispersed) or chromosomal location/mechanism of replication (pericentromeric, telomeric or subtelomeric, microsatellites, minisatellites, satellites, transposable elements, retroelements). Variation in repetitive DNA, manifested as variation in nuclear DNA content, has been shown to have broad ecological and life-history consequences. For example, large genome size appears to limit fitness in extreme environmental conditions. Within species, variation in DNA content has been coupled to growth and development, such as maturation time in crop species. In Silene latifolia, DNA content is negatively correlated with flower size, a character that, in turn, has well documented ecological significance. These intraspecific studies suggest a connection between repetitive DNA and quantitative genetic determination of continuous characters. Novel insights into mechanisms by which repetitive DNA influences phenotype will lead to models of evolutionary change that extend well beyond the conventional view of evolution by allelic substitution. [ABSTRACT FROM AUTHOR]

The development of fruits after pollination places resource demands on plants that may influence the production of subsequent flowers. Pre-dispersal seed predation, resulting in the destruction of developing seeds, may allow resource reallocation to the production of subsequent flowers. Silene latifolia, the white campion, is subject to predispersal seed predation by noctuid moths. In order to determine the potential for resource reallocation in S. latifolia we conducted a greenhouse experiment in which female plants were subjected to three levels of pollination (0%, 50%, or 100%) and simulated pre-dispersal seed predation (0%, 50%, or 100% of total fruit production). We assigned 10 plants to each of the seven treatments (0% pollinated had no fruit); in total, 1490 flowers were measured for flower size and scored for date of flowering and longevity. Flower size decreased over the course of the experiment. Average daily production was 12.2 flowers per plant on nonpollinated plants, but only 4.3 flowers on 100% pollinated plants. Chi-square results showed that simulated seed predation resulted in additional flowering bouts later in the course of the experiment. Time series analysis showed that the time between flowering bouts was also influenced by predation. Plants with 0% predation had an average lag time of 29.5 days, whereas plants with 100% simulated seed predation had a lag period of 20.1 days. Flower longevity of non-pollinated flowers increased in plants that had flowers pollinated but experienced no seed predation. Simulated predation resulted in a decrease in floral longevity. These results suggest that plants reallocate resources to the production of new flowers after the destruction of fruits; thus, flowering phenology is influenced by pollination and seed predation. The relationship between pollinators and flowering phenology is well accepted; these results indicate that seed predators play an equally important role in determining flowering phenology. [ABSTRACT FROM AUTHOR]

Presents information on a study which explored the relationship between sex allocation and sex-specific success in the andromonoecious perennial plant Solanum carolinense. Methodology; Results of the study; Discussion.

Presents a genetic likelihood-based iterative procedure for fractional allocation of paternity within a progeny pool and applies this method to a population of Chamaelirium luteum. Analysis of male reproductive contributions; Nonparametric alternative; Comparison of methods.

Investigates life history traits and resource allocation patterns for both males and females of the dioecious plant Silene latifolia. Impact of fruit production on subsequent allocation to reproduction and growth; Relationship between the amount of biomass allocated to rosette leaves and date that flowering commenced for both females and males.

Investigates the response to sex-specific selection for two sexually dimorphic traits, calyx diameter and flower number in Silene latifolia. Imposition of two generation of sex-specific selection; Direct response of calyx diameter to sex-specific selection; Erratic response of flower number to sex-specific selection.

Explores the relationship between nuclear DNA content, flower size and cell size within and among populations of the American plant -- Silene latifolia (Caryophyllaceae) in order to determine the basis for flower-size variation.

Discusses theories on the higher frequency of unisexual flowers in wind- and water-pollinated species than species that depend on animal pollen vectors. Pollinator limitation hypothesis; Pollinator discrimination against females; Association between unisexuality and mode of pollination; Testing of hypotheses.

Presents a study which assesses the distribution of genetic variation in Chamaecyparis thyoides populations. What the allozyme frequency analyzes; Information on diversity in the results; Indication that there was no correlation between genetic and geographic distances in the populations.

Examines the genetic diversity in Micronesian Island populations of the tropical tree Campnosperma brevipetiolata. Potential economic and social importance of tropical plant species; Awareness of biodiversity loss; Polymorphic genetic loci.

Focuses on the dynamic tension in the perception of evolution in the United States in light of the decision by the Kansas Board of Education to no longer require evolution as part of their school curriculum. Need for a clear understanding of evolutionary biology; Why the public should be informed; Efforts to promote awareness of the contributions of evolutionary biology; The report 'Evolution, Science, and Society: Evolutionary Biology and the National Research Agenda'; Outlook.

Over the last few decades, the nature of life sciences research has changed enormously, generating a need for a workforce with a variety of computational skills such as those required to store, manage, and analyse the large biological datasets produced by next-generation sequencing. Those with such expertise are increasingly in demand for employment in both research and industry. Despite this, bioinformatics education has failed to keep pace with advances in research. At secondary school level, computing is often taught in isolation from other sciences, and its importance in biological research is not fully realised, leaving pupils unprepared for the computational component of Higher Education and, subsequently, research in the life sciences. The 4273pi Bioinformatics at School project (https://4273pi.org) aims to address this issue by designing and delivering curriculum-linked, hands-on bioinformatics workshops for secondary school biology pupils, with an emphasis on equitable access. So far, we have reached over 180 schools across Scotland through visits or teacher events, and our open education resources are used internationally. Here, we describe our project, our aims and motivations, and the practical lessons we have learned from implementing a successful bioinformatics education project over the last 5 years. [ABSTRACT FROM AUTHOR]

Synthesis centers offer a unique amalgam of culture, infrastructure, leadership, and support that facilitates creative discovery on issues crucial to science and society. The combination of logistical support, postdoctoral or senior fellowships, complex data management, informatics and computing capability or expertise, and most of all, opportunity for group discussion and reflection lowers the "activation energy" necessary to promote creativity and the cross-fertilization of ideas. Synthesis centers are explicitly created and operated as community-oriented infrastructure, with scholarly directions driven by the ever-changing interests and needs of an open and inclusive scientific community. The last decade has seen a rise in the number of synthesis centers globally but also the end of core federal funding for several, challenging the sustainability of the infrastructure for this key research strategy. Here, we present the history and rationale for supporting synthesis centers, integrate insights arising from two decades of experience, and explore the challenges and opportunities for long-term sustainability. [ABSTRACT FROM AUTHOR]

Plants provide fundamental support systems for life on Earth and are the basis for all terrestrial ecosystems; a decline in plant diversity will be detrimental to all other groups of organisms including humans. Decline in plant diversity has been hard to quantify, due to the huge numbers of known and yet to be discovered species and the lack of an adequate baseline assessment of extinction risk against which to track changes. The biodiversity of many remote parts of the world remains poorly known, and the rate of new assessments of extinction risk for individual plant species approximates the rate at which new plant species are described. Thus the question ‘How threatened are plants?’ is still very difficult to answer accurately. While completing assessments for each species of plant remains a distant prospect, by assessing a randomly selected sample of species the Sampled Red List Index for Plants gives, for the first time, an accurate view of how threatened plants are across the world. It represents the first key phase of ongoing efforts to monitor the status of the world’s plants. More than 20% of plant species assessed are threatened with extinction, and the habitat with the most threatened species is overwhelmingly tropical rain forest, where the greatest threat to plants is anthropogenic habitat conversion, for arable and livestock agriculture, and harvesting of natural resources. Gymnosperms (e.g. conifers and cycads) are the most threatened group, while a third of plant species included in this study have yet to receive an assessment or are so poorly known that we cannot yet ascertain whether they are threatened or not. This study provides a baseline assessment from which trends in the status of plant biodiversity can be measured and periodically reassessed. [ABSTRACT FROM AUTHOR]

Seasonally dry tropical plant formations (SDTF) are likely to exhibit phylogenetic clustering owing to niche conservatism driven by a strong environmental filter (water stress), but heterogeneous edaphic environments and life histories may result in heterogeneity in degree of phylogenetic clustering. We investigated phylogenetic patterns across ecological gradients related to water availability (edaphic environment and climate) in the Caatinga, a SDTF in Brazil. Caatinga is characterized by semiarid climate and three distinct edaphic environments – sedimentary, crystalline, and inselberg –representing a decreasing gradient in soil water availability. We used two measures of phylogenetic diversity: Net Relatedness Index based on the entire phylogeny among species present in a site, reflecting long-term diversification; and Nearest Taxon Index based on the tips of the phylogeny, reflecting more recent diversification. We also evaluated woody species in contrast to herbaceous species. The main climatic variable influencing phylogenetic pattern was precipitation in the driest quarter, particularly for herbaceous species, suggesting that environmental filtering related to minimal periods of precipitation is an important driver of Caatinga biodiversity, as one might expect for a SDTF. Woody species tended to show phylogenetic clustering whereas herbaceous species tended towards phylogenetic overdispersion. We also found phylogenetic clustering in two edaphic environments (sedimentary and crystalline) in contrast to phylogenetic overdispersion in the third (inselberg). We conclude that while niche conservatism is evident in phylogenetic clustering in the Caatinga, this is not a universal pattern likely due to heterogeneity in the degree of realized environmental filtering across edaphic environments. Thus, SDTF, in spite of a strong shared environmental filter, are potentially heterogeneous in phylogenetic structuring. Our results support the need for scientifically informed conservation strategies in the Caatinga and other SDTF regions that have not previously been prioritized for conservation in order to take into account this heterogeneity. [ABSTRACT FROM AUTHOR]

Understanding which genes have evolved rapidly with the recent tree speciation in arid habitats can provide valuable insights into different adaptation mechanisms. We employed a comparative evolutionary analysis of expressed sequence tags (ESTs) from two desert poplars, Populus pruinosa and P. euphratica, which diverged in the recent past. Following an approach taken previously with P. euphratica, we conducted a deep transcriptomic analysis of P. pruinosa. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of two types of callus and desert-grown trees. De novo assembly generated 114,866 high-quality unique sequences using Solexa sequence data. Following assembly we were able to identify, with high confidence, 2859 orthologous sequence pairs between the two species. Based on the ratio of nonsynonymous (Ka) to synonymous (Ks) substitutions, we identified a total of 84 (2.9%) ortholog pairs exhibiting rapid evolution with signs of strong selection (Ka/Ks>1). Genes homologous to these ortholog pairs in model species are mainly involved in ‘responses to stress’, ‘ubiquitin-dependent protein catabolic processes’, and ‘biological regulation’. Finally, we examined the expression patterns of candidate genes with rapid evolution in response to salt stress. Only one pair of orthologs up-regulated their expression in both species while three and four genes were found to up-regulated in P. pruinosa and in P. euphratica respectively. Our findings together suggest that the genes at the same category or network but with differentiated expressions or functions may have evolved rapidly during adaptive divergence of the two species to differentiated salty desert habitats. [ABSTRACT FROM AUTHOR]

The interface between evolutionary biology and the biomedical sciences promises to advance understanding of the origins of genetic and infectious diseases in humans, potentially leading to improved medical diagnostics, therapies, and public health practices. The biomedical sciences also provide unparalleled examples for evolutionary biologists to explore. However, gaps persist between evolution and medicine, for historical reasons and because they are often perceived as having disparate goals. Evolutionary biologists have a role in building a bridge between the disciplines by presenting evolutionary biology in the context of human health and medical practice to undergraduates, including premedical and preprofessional students. We suggest that students will find medical examples of evolution engaging. By making the connections between evolution and medicine clear at the undergraduate level, the stage is set for future health providers and biomedical scientists to work productively in this synthetic area. Here, we frame key evolutionary concepts in terms of human health, so that biomedical examples may be more easily incorporated into evolution courses or more specialized courses on evolutionary medicine. Our goal is to aid in building the scientific foundation in evolutionary biology for all students, and to encourage evolutionary biologists to join in the integration of evolution and medicine. [ABSTRACT FROM AUTHOR]

Abstract: The distribution, ecology and conservation status of the majority of plant species are poorly known. One of the challenges ahead is to address this knowledge gap and give more emphasis to this important group of species that represents a critical component of earth’s biodiversity. Full conservation assessments require expert knowledge of the group concerned, but for the majority of plant species, especially those from the tropics, the best source of knowledge is specimens housed within herbaria. Digitisation projects are underway to render information from this important global biodiversity resource more accessible; the next step is to assemble and utilise these data to make better informed conservation decisions. One crucial question is: how many herbarium specimens are needed to detect threatened species? Such information would inform and help to prioritise digitisation efforts. Using 11,461 herbarium records we assessed species geographic range to determine a preliminary conservation status of 661 endemic species of Leguminosae and Orchidaceae from Madagascar, following the IUCN criteria. By capturing 15 georeferenced specimens per species we produced range estimates for use in conservation assessments consistent with estimates based on all known specimens, for more than 95% of species. None of the threatened species were misclassified as not threatened, and less than 3% of species would receive conservation support as a result of being falsely identified as threatened. This approach can therefore help progress towards the Global Strategy for Plant Conservation target of a conservation assessment for each plant species, while reducing digitisation effort by up to half. [Copyright &y& Elsevier]

The world's governments have identified reducing the rate of biodiversity loss as a global priority. However, we lack robust measures of progress toward this target. Developing indicators that are generally representative of trends in global biodiversity has presented the scientific community with a significant challenge. Here we discuss the development and implementation of the IUCN Red List Index with a new sampled approach, permitting the assessment of the conservation status and trends of large, speciose taxonomic groups. This approach is based on the IUCN Red List and measures trends in extinction risk through time. The challenges in developing this new approach are addressed, including determining the species groups to be included in the index, identifying the minimum adequate samples size, and aggregating and weighting the index. Implementing this approach will greatly increase understanding of the status of the world's biodiversity by 2010, enabling the first assessment of a number of key groups. [ABSTRACT FROM AUTHOR]