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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.

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.

Funding: Science and Technology Facilities Council (STFC) under Grants ST/R000328 and ST/T000872, the Natural Environment Research Council (NERC) under Grant NE/P000592/1, the Darwin Trust of Edinburgh and the Access for Rural Communities project (ARC) at the University of St Andrews. 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 suggest the workshop is useful and enjoyable, with no 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. Publisher PDF

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This work was supported by CNPq project (455505/2014-4) to all authors; The MPEG/ITVDS/FADESP Term of Agreement (01205.000250/2014-10); DCZ – CNPq productivity grant; NFOM - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (BR- 88887/130640/2016-00). In order to establish effective conservation strategy, drivers of local and regional patterns of biodiversity need to be understood. The composition of local biodiversity is dependent on a number of factors including evolution and redistribution of lineages through dispersal and environmental heterogeneity. Brazilian canga is characterised by a ferrugineous substrate, found both in the Iron Quadrangle of Minas Gerais and in the Carajás mountains in Amazonia. Canga is one of several specialised habitat types comprising Brazilian campo rupestre, a montane vegetation found within or adjacent to several major Brazilian bioregions, including the Atlantic Forest and Amazonia, with exceptionally high levels of diversity and endemism arising from both history of dispersal and environmental variation. In order to inform biodiversity conservation for canga, and more broadly for campo rupestre, we performed floristic and phylogenetic analyses investigating affinities between 28 sites on different substrates (canga and quartzite) and geographic locations (Carajás, Pará [Amazonia]; Cadeia do Espinhaço, Minas Gerais; Chapada Diamantina, Bahia). Through analysis of 11204 occurrences of 4705 species of angiosperms, we found that Amazonian Carajás canga plant communities formed a cohesive group, distinct from species assemblages found in Eastern Brazil (Minas Gerais, Bahia), either on canga or quartzite. The phylogenetic megatree of species across all sites investigated shows associations between certain clades and Amazonian canga, with few shared species between the Amazonian Carajás and Eastern Brazil sites, while the floristic comparison shows high levels of heterogeneity between sites. The need for reserves for Amazonian Carajás canga has been recognized and addressed by the creation of a national park. However, current sampling does not provide sufficient reassurance that the canga areas now benefitting from full legal protection adequately represent the regional canga flora. Publisher PDF

The work was supported by a National Science Foundation Doctoral Dissertation Improvement grant (DEB‐9411513), by the Society for Sigma Xi, and by a Hutcheson Memorial Forest grant. According to Bateman's principle, male fitness in entomophilous plant species should be limited by mating opportunity, which is influenced by the size or number of flowers. We determined male-specific fitness consequences of floral phenotype in andromonoecious Solanum carolinense, examined the relationship between male and female reproductive success within plants, and evaluated the distribution of functional gender among plants. A maximum likelihood-based paternity analysis, based on multilocus allozyme phenotypes of parents and offspring from four experimental plots, was used to determine male reproductive success and its relationship to floral phenotype. Male success was enhanced by an increase in the proportion of male flowers produced but not by an increase in total flower number, even though all flowers contain male parts. Larger flower size increased male success in only one plot. Male and female reproductive success were negatively correlated, and plants varied in functional gender from completely female to completely male. This gender specialization may occur because hermaphroditic and male flowers differ in their ability to contribute to male and female success. Although sex allocation theory predicts a positive relationship between the size or number of plant parts and reproductive success, this study indicates that aspects of floral morphology that affect gender specialization should also be considered. Publisher PDF

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.

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. Postprint

Summary Using TaqMan qPCR assays, DNA of P. ramorum, P. kernoviae and P. austrocedri was detected in 500 g soil samples collected from twelve infected forest and woodland sites in northern Britain. Phytophthora DNA was also amplified in soil adhering to boots after walking transects along footpaths or animal trails. At two sites, Phytophthora DNA was detected in soil over a 4-year period following removal of infected hosts. This new method enabling assessment of larger quantities of soil demonstrates the contamination risk of these pathogens in soil at infected sites and improves our understanding of the mechanisms of persistence and spread.

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.

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.

The distribution of genetic diversity has potential to inform conservation efforts but is rarely incorporated when conservation status is assigned to a species. These data can be beneficial to the conservation assessment process by providing information on subpopulations, gene flow and effective population sizes, thus achieving more successful assessments. In order to obtain a better understanding of the patterns of genetic variation and their relationship to conservation in the fragmented flora of Madagascar, this study assessed genetic diversity among and within Delonix s.l. (Leguminosae) using AFLP markers. The genetic diversity of eight species of Delonix s.l. (covering 79 sample sites and 254 individuals) showed a range of values (25–61% for polymorphic loci, and 0.076–0.192 Shannon’s Index). Results from an analysis of molecular variance (AMOVA) suggest that a majority of the genetic variance is attributed to variation within species (87%), which is also supported by a principle coordinate analysis of genetic distances between sites. The results were used to compare the genetic difference between species of different threat status and show that even closely related species with the same IUCN threat status differ in their genetic structure, probably arising from differences in life history traits, pollen and seed dispersal, and fragmentation. Species that are recently affected by habitat destruction and fragmentation are likely to be at high potential risk of genetic erosion contributing to their ongoing decline. Thus, genetic variation should be taken into consideration in conservation assessments, whenever possible, to provide accurate and targeted conservation recommendations in order to achieve more successful conservation outcomes.

Despite the ecological and economic importance of plants, the majority of plant species and their conservation status are still poorly known. Based on the limited knowledge we have of many plant species, especially those in the tropics, the use of GIS techniques can give us estimates of the degree of population subdivision to be used in conservation assessments of extinction risk. This paper evaluates how best to use the IUCN Red List Categories and Criteria to produce effective and consistent estimates of subpopulation structure based on specimen data available in the herbaria around the world. We assessed population structure through GIS-based analysis of the geographic distribution of collections, using herbarium specimen data for 11 species of Delonix sensu lato. We used four methods: grid adjacency, circular buffer, Rapoport’s mean propinquity and alpha hull, to quantify population structure according to the terms used in the IUCN Red List: numbers of subpopulations and locations, and degree of fragmentation. Based on our findings, we recommend using the circular buffer method, as it is not dependent on collection density and allows points to be added, subtracted and/or moved without altering the buffer placement. The ideal radius of the buffer is debatable; however when dispersal characteristics of the species are unknown then a sliding scale, such as the 1/10th maximum inter-point distance, is the preferred choice, as it is species-specific and not sensitive to collection density. Such quantitative measures of population structure provide a rigorous means of applying IUCN criteria to a wide range of plant species that hitherto were inaccessible to IUCN classification.

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.

† Background and Aims In the present review, I have endeavoured to conduct a joint assessment of the thinking underlying the evolutionary genetics of gender polymorphism and the developmental genetics of gender determination. It is my hope, through highlighting the historical development of ideas in two related but somewhat disparate sets of scientific literature, to encourage a synthetic perspective that integrates the two. † Scope An overview is provided of various theories on the evolution of sex polymorphism and examples of evidence that has been brought to bear in support of them. Current knowledge on floral development is summarized, with an emphasis on gender variation. Finally, an attempt is made to integrate the two perspectives with the hope that it will encourage future research at the interface. † Conclusions Evolutionary models of gender evolution have, of necessity, posited genetic effects that are relatively simple in their impacts. Emerging insights from developmental genetics have demonstrated that the underlying reality is a more complex matrix of interacting factors. The study of gender variation in plants is poised for significant advance through the integration of these two perspectives. Bringing genomic tools to bear on population-level processes, we may finally develop a comprehensive perspective on the evolution of floral gender.

This study was made possible through the kind financial support of the São Paulo Research Foundation - http://fapesp.br/en (Fundação de Amparo à Pesquisa do Estado de São Paulo - Fapesp 2013/15280-9). 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. Publisher PDF

• Background and Aims The overall goal of this paper is to construct an overview of the genetic basis for flower size evolution in Silene latifolia. It aims to examine the relationship between the molecular bases for flower size and the underlying assumption of quantitative genetics theory that quantitative variation is ultimately due to the impact of a number of structural genes. • Scope Previous work is reviewed on the quantitative genetics and potential for response to selection on flower size, and the relationship between flower size and nuclear DNA content in S. latifolia. These earlier findings provide a framework within which to consider more recent analyses of a joint quantitative trait loci (QTL) analysis of flower size and DNA content in this species. • Key Results Flower size is a character that fits the classical quantitative genetics model of inheritance very nicely. However, an earlier finding that flower size is correlated with nuclear DNA content suggested that quantitative aspects of genome composition rather than allelic substitution at structural loci might play a major role in the evolution of flower size. The present results reported here show that QTL for flower size are correlated with QTL for DNA content, further corroborating an earlier result and providing additional support for the conclusion that localized variations in DNA content underlie evolutionary changes in flower size. • Conclusions The search image for QTL should be broadened to include overall aspects of genome regulation. As we prepare to enter the much-heralded post-genomic era, we also need to revisit our overall models of the relationship between genotype and phenotype to encompass aspects of genome structure and composition beyond structural genes.

In insect-pollinated plants, floral characters are expected to play an important role in paternal and maternal reproductive success. Bateman's principle states that male reproductive success increases with more mating opportunities, while female reproductive success is limited by the amount of resources available to produce progeny, thus there should be greater selection on male floral characters than on female. In the case of the dioecious plant Silene latifolia, floral characters are likely to be influenced by its association within its native European range with moths of the genus Hadena, which serve as both pollinators and seed predators. The present study addresses relationships between male and female reproductive success, spatial location and floral characters (corolla, calyx and claw) over a 2-year period in two Spanish populations of S. latifolia in the presence of Hadena moths. A maximum likelihood paternity analysis using genetic variation at six allozyme markers showed heterogeneity in male reproductive success. There was much less variation in female reproductive success. When this analysis was extended to include interplant distance as a causal factor underlying variation in male success, we found that successful pollination tended to be limited to nearby females, in accordance with exponential decay of pollen dispersal with increasing distance. When the paternity analysis included floral characters as a causal factor underlying variation in male success, our data showed little evidence for directional selection, but there was stabilizing selection in one of the two years for calyx diameter. Selection on female characters varied widely between sites and years, in most of the site/year combinations there was little selection on female floral characters; however, in one site/year there was evidence for selection on all three floral characters. We conclude that pollinators visit flowers that are close together, and that while floral characters are important for the attraction of pollinators, larger flowers do not necessarily attract more pollinators at all sites and that variation among sites and years makes difficult any conclusions about the long-term importance of the predictions suggested by Bateman's principle.

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 pre-dispersal 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 non-pollinated 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.

One element of the current public debate about genetically modified crops is that gene flow from transgenic cultivars into surrounding weed populations will lead to more problematic weeds, particularly for traits such as herbicide resistance. Evolutionary biologists can inform this debate by providing accurate estimates of gene flow potential and subsequent ecological performance of resulting hybrids. We develop a model for gene flow incorporating exponential distance and directional effects to be applied to windpollinated species. This model is applied to previously published data on gene flow in experimental plots ofAgrostis stoloniferaL. (creeping bentgrass), which assessed gene flow from transgenic plants resistant to the herbicide glufosinate to surrounding non–transgenic plants. Our results show that although pollen dispersal can be limited in some sites, it may be extensive in others, depending on local conditions such as exposure to wind. Thus, hybridization under field conditions is likely to occur. Given the nature of the herbicide resistance trait, we regard this trait as unlikely to persist in the absence of herbicide, and suggest that the ecological consequences of such gene flow are likely to be minimal.

Creeping bentgrass (Agrostis stolonifera L.) is a commercially important turfgrass used principally on golf courses. Weed control is one of the major problems encountered in golf course maintenance, largely because the major weed, Poa annua L., is another grass species with herbicide responses similar to creeping bentgrass. Development of creeping bentgrass cultivars expressing one of the herbicide resistance genes would provide an effective solution. The prospects of commercialization of transgenic cultivars of creeping bentgrass have raised questions about the potential for pollen-mediated gene flow to related Agrostis spp. In a field study we have measured the frequency of interspecific hybridization between transgenic creeping bentgrass and four related species, A. canina L., A. castellana Boiss. and Reut., A. gigantea Roth, and A. capillaris L. Interspecific transgenic hybrids were recovered between creeping bentgrass and A. capillaris and A. castellana at frequencies of 0.044 and 0.0015%, respectively, which were considerably lower than intraspecific transgenic progeny recovery in the same experimental plots (0.631%). No interspecific transgenic hybrids were recovered with A. gigantea or A. canina.

Investigation of gender specialization in plants has led to several theories on the evolution of sexual dimorphism: reproductive compensation, based on enhanced reproductive efficiency with gender specialization (flowers should be larger on dioecious plants); Bateman's Principle, based on sex-specific selection (display for pollinator attraction in males and seed set in females); and intersexual floral mimicry, based on mimicry of a reward-providing gender by a non-reward providing gender (reduced dimorphism in dioecious plants due to increased spatial separation of male and female flowers). These theories were evaluated in Ecballium elaterium, which contains two subspecies, elaterium (monoecious) and dioicum (dioecious). Our results show that flowers of the dioecious subspecies are larger and allocate more to reproductive organs than do flowers of the monoecious subspecies. Both subspecies are sexually dimorphic (male flowers larger than female flowers). Variance in flower size among populations is greater in the dioecious subspecies. Finally, there is sufficient genetic variation to enable ongoing response to selection; genetic correlation constraints on independent response of female and male flowers may be stronger in the monoecious subspecies. Our findings provide support for aspects of all three theories, suggesting that the evolution of floral dimorphism is based on a complex interplay of factors.

New types of markers, such as RAPDs, microsatellite markers, AFLPs, and SNPs provide the opportunity to obtain information on individuals at multiple genetic loci across the genome. This increase in the number of marker loci has provided enhanced opportunities for statistical analysis of the genetic consequences of genealogical relationship among individuals. In place of the classical models, we can now investigate empirical multilocus segregation patterns. Linkage among loci decreases the precision of relationship estimation but permits additional dimensions of genome sharing to be explored. In this paper we consider the effect of linkage on the pattern of genome sharing among relatives who share (on average) 25% of their dipolid genomes using the empirical meioses giving rise to 58 gametophytes from a single maternal plant of the species Pinus taeda (loblolly pine). The genome sharing among relatives is quantified in terms of the linkage map of the markers.

The present study was conducted to assess the distribution of genetic variation within and among populations of Chamaecyparis thyoides in both marginal and centrally located populations. Allozyme frequency analyses of ten loci from foliage of four New Jersey populations and two North Carolina populations of C. thyoides showed polymorphic loci = 50%, mean number of alleles per locus = 2.8, effective number of alleles per locus = 1.17, and expected heterozygosity = 0.14. Diversity was highest in two populations from southern New Jersey. The isolated population at High Point, New Jersey had only two polymorphic loci and expected heterozygosity of 0.03. There was no correlation between genetic and geographic distances among populations, implying that cedar must have possessed some means of long-distance dispersal at the end of the last glacial period, rather than advancing northward step by step.

Demographic information on natural populations is essential to management of rare species. A comparative demographic study of a rare perennial plant, Eupatorium resinosum, and its closely related common congener, E. perfoliatum, was conducted to examine life history characteristics associated with rarity. Demography of three natural populations of each species revealed that E. resinosum has relatively lower sexual and asexual reproduction but more successful establishment of seedlings and asexually produced ramets than E. perfoliatum. Matrix projection analysis showed positive projected growth rates for two populations of E. resinosum, whereas E. perfoliatum showed a positive projected growth rate in only one of the populations studied. Survivorship of nonflowering ramets influenced projected population growth rates more in E. resinosum, while survivorship of flowering individuals influenced projected population growth rates more in E. perfoliatum. E. resinosum appears able to maintain populations in the short term, but over the long term lower seed production may make it difficult for E. resinosum to colonize new habitats as frequently as E. perfoliatum.

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.

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. Publisher PDF

Tropical plant species have been the focus of considerable attention in regard to their potential economic and social importance in the face of rapidly diminishing biodiversity in the tropics. Pacific Island species represent an even more fragile resource because different island populations are widely scattered and overall population sizes are small. We examined the distribution of genetic variation in Campnosperma brevipetiolata (Anacardiaceae), an upland rainforest tree species that is of potential use for both lumber and reforestation efforts in the Federated States of Micronesia (FSM). Seeds were collected from multiple populations on four island groups in the Caroline Islands (Kosrae, Pohnpei, and Yap in the FSM; and the Republic of Palau) and subjected to an electrophoretic analysis involving four polymorphic genetic loci. We hypothesized that variation on these islands would decrease with increasing distance from the presumed Indo-Malayan source of these island floras. Indeed, we found a trend of decreasing variation from west to east indicated by the mean number of alleles per locus (A = 1.50-1.33), effective number of alleles per locus (A, = 1.14-1.12) and mean genetic diversity (He = 0.1230.107). We also found little genetic differentiation among the islands (Fp, = 0.174) and among subpopulations within islands (Fsp = 0.047), indicating that either there are high levels of gene flow among the islands by seed dispersal or that these populations have not been established long enough for divergence to have occurred. The lack of divergence among islands observed for Campnosperma brevipetiolata suggests that germplasm sampled from any one island population would be a suitable starting point for plant breeding or reforestation efforts.

Nuclear DNA content shows extensive intraspecific variation in plants, attributable to changes in levels of repetitive DNA. Since its discovery, repetitive DNA often has been regarded as `junk' or selfish DNA with little or no evolutionary significance at the individual level, except possibly a deleterious role stemming from its over-replication. However, recent works have pointed out that repetitive DNA may have an important impact on phenotypic selection through local or general modifications of gene expression. Phenotypic evolution has typically been studied using quantitative genetic techniques that treat underlying genetic effects as variance components. In previous work, we identified an among population negative correlation between nuclear DNA content variation, attributable to repetitive DNA, and calyx diameter, a phenotypic character with obvious ecological importance, in Silene latifolia. In the present study, we established a negative genetic relation between an AT-biased flow cytometric measure of nuclear DNA content and calyx diameter across lineages that had been subjected to selection for increases or decreases in calyx diameter. This finding suggests that new attention should be directed toward repetitive DNA as a basis for phenotypic variation and evolution.

Females of dioecious plant species are expected to show greater trade-offs with other life history traits than males because of their high investment in reproduction. We investigated life history traits and resource allocation patterns for both males and females of the dioecious plant Silene latifolia, to document allocation both prior to and after re- productive investment. In addition, the impact of fruit production on subsequent allocation to reproduction and growth was investigated by varying the number of flowers pollinated on females. The mean date of first reproduction was the same for males and females. Early- flowering plants of both sexes invested less in leaf biomass than plants that delayed flow- ering. The percentage of flowers pollinated had a significant effect on how resources were allocated, and on the amount and timing of further flower production. Sexual dimorphism was observed in resource allocation patterns after, but not prior to, investment in repro- duction. Overall, pollinated females were found to have more leaf biomass and invest nearly twice as much in reproduction as males, in spite of an apparent trade-off between leaf production and reproduction within both females and males. We conclude that sexual di- morphism in life history traits that affects resource acquisition causes the resource pool that is allocated to be variable, rather than static, thereby masking the underlying trade- offs.

Genealogical analysis is a powerful tool for analysis of reproductive performance in both natural and captive populations, but assignment of paternity has always been a stumbling block for this sort of work. Statistical methods for determining paternity have undergone several phases of development, ranging from straightforward genetic exclusion to assignment of paternity based on genetic likelihood criteria. In the present study, we present a genetic likelihood-based iterative procedure for fractional allocation of paternity within a progeny pool and apply this method to a population of Chamaelirium luteum, a dioecious member of the Liliaceae. Results from this analysis clearly demonstrate that different males make unequal contributions to the overall progeny pool, with many males contributing essentially nothing to the next generation. Furthermore, the distribution of paternal success among males shows a highly significant departure from (Poisson) randomness. The results from the present analysis were compared with earlier results obtained from the same data set, using likelihood-based categorical paternity assignments. The general biological pattern revealed by the two analyses is the same, but the estimates of reproductive success are only modestly (though significantly) correlated. The iterative procedure makes more complete use of the data and generates a more sharply resolved distribution of male reproductive success.

The technique of DNA flow cytometry was used to study variation in DNA content among different ploidy levels, as well as among diploid species, of Vaccinium section Cyanococcus. In a sample of plants of varying ploidy level, the relative fluorescence intensity (RFI) of nuclei stained with propidium iodide was a function of the number of chromosome sets (x), as represented by the linear equation RFI=3.7x-2.3 (r(2)=95%). The data indicated that DNA flow cytometry could be useful for the determination of ploidy level at the seedling stage in blueberry. They also suggest that "conventional polyploid evolution" has occurred in this section of the genus Vaccinium with an increase in nuclear DNA content concurrent with the increase in chromosome number. The nuclear DNA content of diploid species of Vaccinium section Cyanococcus was estimated from the relationship of the observed RFI to an internal known DNA standard (trout red blood cells). A nested analysis of variance indicated significant variation among species, as well as among populations within species, in nuclear DNA content, although this variation was small compared to the variation among ploidy levels. The variation in nuclear DNA content corresponded to the phylogenetic relationships among species determined from previous studies.

Dioecy, the separation of sexes, has arisen independently many times in the course of angiosperm evolution. Avoidance of inbreeding is clearly involved in the evolution of dioecy, and as a consequence we predict that dioecious populations should maintain higher levels of genetic variation than closely related nondioecious populations. We tested that prediction by comparing allozymic variation in two closely related taxa, the monoecious and dioecious subspecies of the Mediterranean cucurbit, Ecballium elaterium. Thirteen polymorphic loci were screened for seeds sampled from 10 monoecious and 13 dioecious populations spanning the geographic ranges of the subspecies in Spain. The dioecious subspecies showed strikingly greater allelic diversity and heterozygosity than the monoecious subspecies. A hierarchical F-statistic analysis clearly demonstrated considerable genetic variation within populations for the dioecious populations, whereas for the monoecious populations almost all genetic variation resulted from differences among populations. The general pattern of homozygosity within monoecious populations suggests that they are highly inbred. In order to assess historical influences on current patterns of genetic variation, we conducted a genetic-distance analysis. The observed relationship between genetic distance and geographic distance between populations supports the hypothesis that the subspecies’ current allopatric distributions on the Iberian Peninsula are the result of separate waves of colonization from the north (monoecious) and south (dioecious).

It is widely recognized that there are basic conflicts between the resource needs of a plant for paternal versus maternal functions. In dioecious species, these divergent demands, and the selection pressures they impose, can lead to the evolution of sexual dimorphism. The present study was conducted to assess the potential for the evolution of sexual dimorphism in Silene latifolia by evaluating the genetic variation and genetic correlation between characters and between the sexes for a range of growth and reproductive characters. Sexual dimorphism is largely restricted to reproductive characters, particularly flower number and flower size. A canonical correlation analysis revealed considerable intercorrelation between growth characters, such as germination date, height, and leaf size, and reproductive characters; plants that grow fast early on also flower earlier, and plants that produce big leaves also produce big flowers. There was genetic variation for several sexually dimorphic characters; much of the focus in this analysis was on flower size, particularly calyx diameter. Finally, genetic correlations within and between the sexes were found that limit the rate of evolutionary divergence between the sexes. The genetic results suggest that S. latifolia has been subject to divergent selection on the two sexes for a long period of time, bringing about a gradual fixation of sex-limited gene effects, so that the remaining genetic effects are expressed in both sexes. Genetic correlations between the sexes that arise from this residual variation impose limits on further evolutionary change.

Mate availability in small populations of plant species with homomorphic sporophytic self-incompatibility

Sex identification in dioecious plants using nonflowering material would have broad applications in both basic and applied research. We present a method using flow cytometry for diagnosing the sex of the dioecious speciesSilene latifolia Poiret (Caryophyllaceae) by means of sexual differences in nuclear DNA content and base-pair composition. Males have a significantly larger genome, attributable to the known sex-chromosome heteromorphism. Males and females also differ in the AT/GC composition, attributable to differences in non-recombining portions of the sex chromosomes. The two measures enable assignment of individuals to sex with a combined error rate of 9%. These results forS. latifolia indicate useful directions for future research into sex diagnostics for other dioecious species.

Male reproductive success in plant populations can be influenced by resources invested in reproductive effort, competition for mating opportunities, and the quality of female mates available. I analyzed the relationship between such ecological factors and male success within a single large population of the dioecious plant Chamaelirium luteum. Male reproductive success had been determined in a previous study using genetic likelihoods of paternity. In the present analysis, no apparent relationship was found between male size (indicative of reproductive effort) and paternal success. An alternating pattern of negative and positive spatial autocorrelation in success was found for the first through tenth nearest neighbors, suggesting local competition among males for matings. Availability of females, as reflected in localized sex ratios, had little influence on male success. Finally, the size of local females, which could limit male success by limiting the total possible seed output, was not related to male su...

SummaryOne of the long-standing mysteries in genomic evolution is the observation that much of the genome is composed of repetitive DNA, resulting in inter- and intraspecific variation in nuclear DNA content. Our discovery of a negative correlation between nuclear DNA content and flower size inSilene latifoliahas been supported by our subsequent investigation of changes in DNA content as a correlated response to selection on flower size. Moreover, we have observed a similar trend across a range of related dioecious species inSilenesect.Elisanthe. Given the presence of sex chromosomes in dioeciousSilenespecies, and the tendency of sex chromosomes to accumulate repetitive DNA, it seems plausible that dioecious species undergo genomic evolution in ways that differ from what one might expect in hermaphroditic species. Specifically, we query whether the observed relationship between nuclear DNA content and flower size observed in dioeciousSileneis a peculiarity of sex chromosome evolution. In the present study we investigated nuclear DNA content and flower size variation in hermaphroditic species ofSilenesect.Siphonomorpha, as close relatives of the dioecious species studied previously. Although the nuclear DNA contents of these species were lower than those for species in sect.Elisanthe, there was still significant intra- as well as interspecific variation in nuclear DNA content. Flower size variation was found among species of sect.Siphonomorphafor petal claw and petal limb lengths, but not for calyx diameter. This last trait varies extensively in sect.Elisanthe, in part due to sex-specific selection. A negative correlation with nuclear DNA content was found across populations for petal limb length, but not for other floral dimensions. We conclude that impacts of nuclear DNA content on phenotypic evolution do manifest themselves in hermaphroditic species, so that the effects observed in sect.Elisanthe, and particularly inS. latifolia, while perhaps amplified by the genomic impacts of sex chromosomes, are not limited to dioecious taxa.

The present study focussed on the moss species, Climacium americanum Brid., which typically grows in the form of mats or clumps of compactly spaced gametophores. In order to determine the clonal structure of these clumps, the distribution of genetic variation was analysed by an electrophoretic survey. Ten individua! gametophores from each of ten clumps were sampled in two locations in the Piedmont of North Carolina. These samples were assayed for allelic variation at six electrophoretically distinguishable loci. For each clump, an explicit probability of a monomorphic versus a polymorphic sample was estimated based on allele frequencies in our overall sample. Although allelic variation was detected within clumps at both localities, our statistical results showed that the level of polymorphism within clumps was less than would be expected if genetic variation were distributed at random within the overall population.