A maximum likelihood approach to the detection of selection from a phylogeny

Summary A large amount of information is contained within the phylogentic relationships between species. In addition to their branching patterns it is also possible to examine other aspects of the biology of the species. The influence that deleterious selection might have is determined here. The likelihood of different phylogenies in the presence of selection is explored to determine the properties of such a likelihood surface. The calculation of likelihoods for a phylogeny in the presence and absence of selection, permits the application of a likelihood ratio test to search for selection. It is shown that even a single selected site can have a strong effect on the likelihood. The method is illustrated with an example fromDrosophila melanogaster and suggests that delerious selection may be acting on transposable elements.     

Relationships between flowering phenology,plant size and reproductive success in shape Lotus corniculatus (Fabaceae)

Over three years the flowering phenology of individuals of Lotus corniculatus has been studied in relation to fruit set and seed predation to determine the relationships between four components of flowering time, plant size and reproductive success. Timings of first and peak flowering, and duration and synchrony of flowering differed between individuals in the same years. Between years, timing of first flowering was highly correlated for the same individuals, and was closely correlated with plant size and duration of flowering–larger plants flowered earlier and for a longer period. Peak flowering and synchrony were not correlated between-years for individuals.Fruit production and seed predation were correlated with some of the components of flowering phenology in some years, but not in others. The inconstancy of these relationships suggests that directional or stabilising selection is not acting consistently on the aspects of reproductive success studied in this work. The inconstancy of selection may result in the rather asynchronous flowering phenologies of individuals of L. corniculatus observed.We emphasize the importance of studying different components of flowering phenology in relation to individual plant size over several seasons. This work has shown that plant size not only has a direct effect on individual plant fecundity but also can influence flowering time and hence indirectly affect reproductive output.     

Divergent selection on flowering time contributes to local adaptation in Mimulus guttatus populations

The timing of when to initiate reproduction is an important transition in any organism's life cycle. There is much variation in flowering time among populations, but we do not know to what degree this variation contributes to local adaptation. Here we use a reciprocal transplant experiment to examine the presence of divergent natural selection for flowering time and local adaptation between two distinct populations of Mimulus guttatus. We plant both parents and hybrids (to tease apart differences in suites of associated parental traits) between these two populations into each of the two native environments and measure floral, vegetative, life-history, and fitness characters to assess which traits are under selection at each site. Analysis of fitness components indicates that each of these plant populations is locally adapted. We obtain striking evidence for divergent natural selection on date of first flower production at these two sites. Early flowering is favored at the montane site, which is inhabited by annual plants and characterized by dry soils in midsummer, whereas intermediate (though later) flowering dates are selectively favored at the temperate coastal site, which is inhabited by perennial plants and is almost continually moist. Divergent selection on flowering time contributes to local adaptation between these two populations of M. guttatus, suggesting that genetic differentiation in the timing of reproduction may also serve as a partial reproductive isolating barrier to gene flow among populations.     

The effectiveness of some mechanisms of reproductive isolation in Arum maculatum and A. italicum (Araceae)

Mechanisms of reproductive isolation were studied in two species of Arum , A. italicum and A. maculatum , growing in England and the south of France. The study focused on three potential mechanisms for reproductive isolation: the effectiveness of dichogamy as a barrier to autogamy; the ability of self and outcrossed pollen to germinate on stigmas at different stages of anthesis and to effect pollination; and postzygotic barriers to selfing. Dichogamy was found to provide a very effective barrier to within-inflorescence selfing in these species, as no seeds were produced by spontaneous self-pollination (i.e. autogamy) in any population of either species. However, the study found that geitonogamy (cross-pollination between inflorescences of a same individual or clone) was possible, as genotypes frequently produced several inflorescences and stigmas were found to be receptive to pollen from before anthesis until their contraction at the end of the female phase of flowering. Hand pollination with self pollen from clone inflorescences produced as numerous and heavy seeds as outcross pollination. In addition, the germination and growth of geitonogamously produced seed was similar to that of outcrossed seed, suggesting that this potential postzygotic barrier is absent or weak. These findings suggest that geitonogamous seed production may be unrestricted by significant pre- or postzygotic barriers. The possible advantages of geitonogamy in Arum are discussed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 323–328.     

Evidence of genetic influence on the flowering pattern of Ficus microcarpa

Flowering patterns result from the interactions between genetic and environmental factors. While the genetic basis for flowering time variation in commercial plants is often well understood, few studies have been conducted to investigate these patterns in plants without economic importance. Ficus microcarpa is a commonly introduced horticultural fig tree. Asynchrony in syconium development and the initiation, frequency, and size of crops may affect its fitness as well as the success of mutualism with its pollinating wasps. In order to identify genetically determined patterns in the flowering traits in F. microcarpa, a 14-month census was taken on the flowering characteristics of 28 trees growing in close proximity along an urban street in Taipei, Taiwan. Weekly surveys were taken on 7 characteristics: crop number, syconia per branch, crop asynchrony, as well as flowering onset and seed development duration for both the spring and summer crops. Post-census genotyping at microsatellite loci distinguished 16 genetic groups (5 clonal groups and 11 non-clone trees). All crop characteristics presented higher variation across different genotype groups than within groups except for seed development duration. We found no evidence of adjacency effects or spatial auto-correlation of flowering traits. The study offers the first evidence of genetic variations in the flowering patterns in a species of Ficus. These findings lend insight into the adaptive characteristics that potentially facilitate the local establishment of F. microcarpa in new locations.     

Rainfall and flowering synchrony in a tropical shrub: Variable selection on the flowering time ofErythroxylum havanense

Summary We tested the adaptive significance of flowering synchrony by means of a quantitative analysis of selection and by flowering induction experiments with the deciduous shrubErythroxylum havanense. Temporal schedules of flower and fruit production were determined for a local population (in three sites) in a Mexican seasonal forest for 2 years (1987–1988). The consequences of natural variation in flowering time (flowering initiation day) on maternal reproductive success (fecundity) were evaluated. We observed high levels of inter- and intraindividual flowering synchrony in 1987, but not in 1988 and this contrast was related to differences in rainfall patterns between the two years. A significant proportion (15.4%) of the phenotypic variation in flowering initiation day was accounted for by environmental variance. The expression of phenotypic variance of flowering time and, consequently, the opportunity for selection to act, are controlled by annual variation in rainfall. Despite the between-year difference in flowering synchrony, we detected a relatively intense directional selection on flowering initiation day in both years, but selection coefficients were of opposite sign (standardized directional gradients were –0.326 and 0.333 for 1987 and 1988, respectively). For both years there was a significant relationship between individual relative fitness and the number of neighbouring flowering plants in a given day, suggesting positive frequency-dependent selection.     

Reproductive biology of Arum italicum (Araceae) in the south of France

The reproductive success of Arum italicum in south-western France showed a positive relationship with plant vigour at both the plant (number of inflorescences) and inflorescence (number of seeds) levels. However, the infructescence and berry numbers were not related to the number of inflorescences, and two-fold more seeds were produced by individuals flowering several times than by those flowering just once. Moreover, the reproductive success of this species appeared to be limited by the high abortion rate (50%), strong predation pressure on the inflorescences (34%), and low seed set rate of nonpredated inflorescences (36%), suggesting pollination limitation. Nevertheless, a positive relationship was found between the mean number of Psychoda trapped per inflorescence and the number of maturing infructescences, particularly for the most abundant species, Psychoda crassipenis . Therefore, pollinator availability appeared to be an important limiting factor for fructification in the studied population, by contrast with other studies in which the fruit set appeared to be related more strongly to the density of inflorescences. Such different results may have been caused by the relatively low abundance of Psychoda in the present study.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 43–49.     

The design of trapping devices in pollination traps of the genus Arum (Araceae) is related to insect type

Pollinators have long been known to select for floral traits, but the nature of this relationship has been little investigated in trap pollination systems. We investigated the trapping devices of 15 Arum spp. and compared them with the types of insects trapped. Most species shared a similar general design of trap chamber walls covered in downward‐pointing papillate cells, lacunose cells in the chamber wall and elongated sterile flowers partially blocking the exit of the trap. However, there was significant variation in all these morphological features between species. Furthermore, these differences related to the type of pollinator trapped. Most strikingly, species pollinated by midges had a slippery epidermal surface consisting of smaller papillae than in species pollinated by other insects. Midge‐pollinated species also had more elongated sterile flowers and tended to have a larger lacunose area. We conclude that pollination traps evolve in response to the type of insect trapped and that changes to the slippery surfaces of the chamber wall are an important and previously little recognized variable in the design of pollination traps. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 385–397.     

Flowering dynamics in Arum italicum (Araceae): relative role of inflorescence traits, flowering synchrony, and pollination context on fruit initiation

We studied the relative role of inflorescence traits, flowering synchrony, and pollination context for infructescence and fruit initiation in two Spanish populations of Arum italicum, a species in which inflorescences are the pollination unit. In this species, a specialized inflorescence organ, the appendix, is important for pollinator attraction. However, the short floral longevity and the production of mostly one inflorescence per plant make its pollination potentially dependent on strong flowering synchrony and on external factors not controlled by the plant (the pollination context). The flowering period in both sites lasted >3 mo. Day-to-day variation in simultaneous antheses was high, and 11-50% of antheses occurred on days during which no pollen donor was present. Inflorescence traits, flowering synchrony, and between-plant distance all influenced infructescence and fruit initiation, but their relative importance differed between sites. In one large population, infructescence initiation was positively related to inflorescence traits; in a smaller population infructescence initiation increased with the number of donor inflorescences. In both sites, percentage of fruits initiated per infructescence was dependent on a combination of inflorescence traits, flowering synchrony, and between-plant distance. Plants producing 2-4 inflorescences had higher probability of infructescence initiation and overlapped their antheses with more plants than single-inflorescence ones.     

Modification of phenotypic and functional gender in the monoecious Arum italicum (Araceae)

Other than studies on sex-labile Arisaema species, studies of gender patterns in Araceae are scarce. The modification of phenotypic and functional gender was investigated in three populations of the monoecious Arum italicum Miller. The probability of reproduction and the number of inflorescences produced increased with plant size, and flower number (total, male, staminodes, female, pistillodes) increased with both plant and inflorescence sizes. However, plant and inflorescence sizes were poor predictors of floral sex ratio (female to male flower ratio). In contrast, change in floral sex ratio towards increasing femaleness was found among inflorescences sequentially produced by a plant. This change could not be explained by either a decrease in inflorescence size or a change in the mating environment. Differences in functional gender did not appear to be related to plant size or stage in the flowering period. Instead, different patterns of functional gender were found between plants with different number of inflorescences. Multi-inflorescence plants showed a functional gender around 0.5, while plants with one inflorescence showed a more extreme functional gender (either male, female, or functionally sterile). Sex of flowers in this species did not seem to exhibit a phenotypic trade-off.     

Natural phenological variation in aspen (Populus tremula): the SwAsp collection

The genus Populus is currently the main model system for genetic, genomic, and physiological research in trees. Phenotypic variation in aspen (Populus tremula) populations growing in different environments across Sweden is expected to reflect genetic variation that is important for local adaptation. To analyze such natural phenotypic and genetic variation, the Swedish Aspen (SwAsp) Collection was established. Trees were taken from 12 different populations across Sweden, from 56° to 66° latitude north and planted in two common gardens in Ekebo (55.9°N) and Sävar (63.4°N). Data related to phenological and growth traits were collected during the second year of growth. Some traits like the date of bud set and leaf area duration showed strong clinal variation patterns with latitude in both field trials, but the date of bud flush did not change along a latitudinal cline. The phenological traits showed moderate within-populations heritabilities, although growth traits showed weaker clinal patterns and lower heritabilities than the phenological traits. This research forms the starting point for the development of the SwAsp collection, a resource facilitating analysis of the natural genetic variation in aspen, the elucidation of the structure and dynamics of aspen populations, and the future identification of the genes controlling adaptive traits using association mapping of selected candidate genes.     

Living on the edge: Fig tree phenology at the northern range limit of monoecious Ficus in China

Fig trees (Ficus) are a species-rich group of mainly tropical and subtropical plants that are of ecological importance because of the large numbers of vertebrates that utilise their figs for food. Factors limiting their distributions to warmer regions are still poorly understood, but are likely to include factors linked to their specialised pollination biology, because each Ficus species is dependent on one or a small number of host-specific fig wasps (Agaonidae) for pollination. Adult fig wasps are short-lived, but some species are capable of dispersing extremely long distances to pollinate their hosts. Close to its northern range limit we investigated the phenology of Ficus virens, the monoecious fig tree that reaches furthest north in China. Relatively few trees produced any figs, and very few retained figs throughout the winter. Despite this, new crops produced in spring were pollinated, with seasonally migrant pollinators from plants growing further south the most likely pollen vectors. An inability to initiate new crops at low temperatures may limit the distribution of monoecious fig trees to warmer areas.     

Phylogeny and Bayesian divergence time estimations of small-headed flies (Diptera: Acroceridae) using multiple molecular markers

The first formal analysis of phylogenetic relationships among small-headed flies (Acroceridae) is presented based on DNA sequence data from two ribosomal (16S and 28S) and two protein-encoding genes: carbomoylphosphate synthase (CPS) domain of CAD (i.e., rudimentary locus) and cytochrome oxidase I (COI). DNA sequences from 40 species in 22 genera of Acroceridae (representing all three subfamilies) were compared with outgroup exemplars from Nemestrinidae, Stratiomyidae, Tabanidae, and Xylophagidae. Parsimony and Bayesian simultaneous analyses of the full data set recover a well-resolved and strongly supported hypothesis of phylogenetic relationships for major lineages within the family. Molecular evidence supports the monophyly of traditionally recognised subfamilies Philopotinae and Panopinae, but Acrocerinae are polyphyletic. Panopinae, sometimes considered "primitive" based on morphology and host-use, are always placed in a more derived position in the current study. Furthermore, these data support emerging morphological evidence that the type genus Acrocera Meigen, and its sister genus Sphaerops, are atypical acrocerids, comprising a sister lineage to all other Acroceridae. Based on the phylogeny generated in the simultaneous analysis, historical divergence times were estimated using Bayesian methodology constrained with fossil data. These estimates indicate Acroceridae likely evolved during the late Triassic but did not diversify greatly until the Cretaceous.     

New insights into the phylogenetics and biogeography of Arum (Araceae): unravelling its evolutionary history

The heat‐ and odour‐producing genus Arum (Araceae) has interested scientists for centuries. This long‐term interest has allowed a deep knowledge of some complex processes, such as the physiology and dynamics of its characteristic lure‐and‐trap pollination system, to be built up. However, mainly because of its large distributional range and high degree of morphological variation, species' limits and relationships are still under discussion. Today, the genus comprises 28 species subdivided into two subgenera, two sections and six subsections. In this study, the phylogeny of the genus is inferred on the basis of four plastid regions, and the evolution of several morphological characters is investigated. Our phylogenetic hypothesis is not in agreement with the current infrageneric classification of the genus and challenges the monophyly of several species. This demonstrates the need for a new infrageneric classification based on characters reflecting the evolution of this enigmatic genus. To investigate the biogeography of Arum deeply, further spatiotemporal analyses were performed, addressing the importance of the Mediterranean basin in the diversification of Arum. Our results suggest that its centre of origin was the European–Aegean region, and that major diversification happened during the last 10 Myr. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 14–32.     

Directional selection on initial flowering date in Phlox drummondii (Polemoniaceae)

The fitness effects due to initial flowering date in Phlox drummondii were determined for three populations in central Texas (USA) over 3 yr (1990-1992). Mean fitness (seed set) always decreased with the later initiation of flowering. The likelihood of a plant fruiting differed with flowering date in five of the six instances (population by year combinations). Though plants that initiated flowering later tended to have spent more time in the vegetative stage and tended to die later in the year than did earlier flowering plants, this was not sufficient to overcome the reproductive penalties of flowering late. Plants that initiated flowering later in the season spent less time in the adult phase and were smaller. The mean number of flowers, fruits, and seeds per flowering plant always decreased with later flowering. Fruit set was negatively correlated with flowering date in four of the six population by year combinations. Nonparametric fitness functions were used to summarize predicted fitness among different initial flowering dates for each population on a yearly basis. Predicted mean fitness always declined nonlinearly with later flowering; the earliest flowering plants always had the highest predicted fitness. These fitness functions describe directional selection for the early initiation of flowering.     

Within‐plant variation in reproductive investment: consequences for selection on flowering time

Variation among the leaves, flowers or fruit produced by a plant is often regarded as a nuisance to the experimenter and an impediment to selection. Here, we suggest that within‐plant variation can drive selection on other plant‐level traits. We examine within‐plant variation in floral sex allocation and in fruit set and predict that such variation generates variation in male success among plants, thereby driving selection on flowering time. We tested this prediction in a simulation model estimating selection on flowering time through male fitness when floral sex allocation and/or fruit set vary directionally among flowers on plants. We parameterized the model through a quantitative literature survey of within‐plant change in sex allocation. As predicted, within‐plant variation in floral sex allocation and in fruit set probability can generate selection on flowering time through male fitness. Declining fruit set from first to last flowers on plants, as occurs in many species, selected for early flowering onset through male fitness. This result was robust to self‐incompatibility and to varying returns on male versus female investment. Selection caused by declining fruit set was strong enough to reverse the selection for late flowering that can be caused by intrafloral protandry. Our model provides testable predictions regarding selection on flowering time through male fitness. The model also establishes the intriguing possibility that within‐plant variation may influence selection on other traits, regardless of whether that variation is under selection itself.     

Evidence for balancing selection acting on KIR2DL4 genotypes in rhesus macaques of Indian origin

The interaction of killer-cell immunoglobulin-like receptors (KIR) and their respective major histocompatibility complex (MHC) ligands can alter the activation state of the natural killer (NK) cell. In both humans and rhesus macaques, particular types of non-classical MHC class I molecules are predominantly expressed on the trophoblast. In humans, human leukocyte antigen G has been demonstrated to act as a ligand for KIR2DL4, present on all NK cells, whereas Mamu-AG may execute a similar function in rhesus macaques. During primate evolution, orthologues of KIR2DL4 appear to have been highly conserved, suggesting strong purifying selection. A cohort of 112 related and unrelated rhesus macaques of mostly Indian origin were selected to study their KIR2DL4 genes for the occurrence of polymorphism. Comparison of the proximal region provided evidence for strong conservative selection acting on the exons encoding the Ig domains. As is found in humans, in the Indian rhesus macaque population, two different KIR2DL4 entities are encountered, which differ for their intra-cellular signalling motifs. One genotype contains a complex mutation in the distal region of exon 9, which negates a serine/threonine kinase site. Furthermore, both allelic entities are present in a distribution, which suggests that balancing selection is operating on these two distinct forms of KIR2DL4. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of Sexual Reproduction on Growth and Vegetative Propagation in the Perennial Geophyte Arum italicum (Araceae)

Abstract: The influences of sexual reproduction on growth and vegetative propagation were analysed in three populations of the geophyte Arum italicum Miller (Araceae). In an observational study using multiple regression, a negative influence of repro duction on tuber mass was detected for two populations. In an experimental study, "control" and "inflorescence removal" treatments were imposed on plants from one of the popula tions. Tuber growth was significantly lower in "control" plants than in "removal" plants, indicating the existence of a somatic cost of reproduction. The somatic cost of reproduction was de creased by an increasing degree of temporal coincidence be tween leaves and reproductive structures on the l)laflt. Neither the observational nor the experimental studies showed any neg ative effect of sexual reproduction on vegetative propagation.     

Floral development of Urospatha: merosity and phylogeny in the Lasioideae (Araceae)

In this paper we study merosity in the genus Urospatha within the framework of a resolved phylogeny of the Araceae. We analyse how a transition from dimerous or tetramerous merosity to pentamerous or hexamerous merosity can occur developmentally in the Lasioideae. In Urospatha, initiation of floral primordia along the inflorescence is acropetal, while development of flowers is basipetal. This indicates the presence of two distinct phases in the development of the Urospatha inflorescence. The first phase corresponds to initiation of flowers and establishment of the phyllotactic pattern, and the second phase to differentiation of floral organs. Urospatha is characterized by the presence of trimerous, tetramerous, pentamerous and rarely hexamerous flowers. In all types of flowers, the stamens are closely associated and opposite to the tepals. Pentamerous flowers are formed by addition of a sector comprising a stamen and tepal. Likewise, in the case of hexamerous flowers, two sectors are added. In the Lasioideae, the increase in the number of tepals and stamens is linked with two developmental processes that have appeared independently in the subfamily: (1) addition of one or two stamen?Cpetal sectors (Anaphyllopsis and Urospatha), and (2) independent increase in the number of tepals and stamens on whorls, more or less organized and inserted in alternate position (Dracontium). Tetramerous whorls as they occur in basal Lasioideae would be homologous to two dimerous whorls from an evolutionary point of view.     

Four decades of opposing natural and human-induced artificial selection acting on Windermere pike (Esox lucius)

The ability of natural selection to drive local adaptation has been appreciated ever since Darwin. Whether human impacts can impede the adaptive process has received less attention. We tested this hypothesis by quantifying natural selection and harvest selection acting on a freshwater fish (pike) over four decades. Across the time series, directional natural selection tended to favour large individuals whereas the fishery targeted large individuals. Moreover, non-linear natural selection tended to favour intermediate sized fish whereas the fishery targeted intermediate sized fish because the smallest and largest individuals were often not captured. Thus, our results unequivocally demonstrate that natural selection and fishery selection often acted in opposite directions within this natural system. Moreover, the two selective factors combined to produce reduced fitness overall and stronger stabilizing selection relative to natural selection acting alone. The long-term ramifications of such human-induced modifications to adaptive landscapes are currently unknown and certainly warrant further investigation.