Genome-wide patterns of large-size presence/absence variants in sorghum

The presence/absence variants （PAVs） are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L.） genomes, each 12？ coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size （＆gt;30 kb） PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96＆amp;nbsp;sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.     

THE ROLE OF INBREEDING DEPRESSION AND MATING SYSTEM IN THE EVOLUTION OF HETEROSTYLY

We investigated the role of morph‐based differences in the expression of inbreeding depression in loss of the mid‐styled morph from populations of tristylous Oxalis alpina. The extent of self‐compatibility (SC) of reproductive morphs, the degree of self‐fertilization, and the magnitude of inbreeding depression were investigated in three populations of O. alpina differing in their tristylous incompatibility relationships. All three populations exhibited significant inbreeding depression. In two populations with highly modified tristylous incompatibility, manifested as increased reciprocal compatibility between short‐ and long‐styled morphs, substantial SC and self‐fertilization of mid‐styled morphs were detected, and expected to result in expression of inbreeding depression in the progeny of mid‐styled morphs in the natural populations. In contrast, significant self‐fertility of the mid‐styled morph was absent from the population with typical tristylous incompatibility, and no self‐fertilization could be detected. Although self‐fertilization and expression of inbreeding depression should result in selection against the mid‐styled morph in the later stages of the transition from tristyly to distyly, in O. alpina selection against the mid‐styled morph in the early phases of the evolution of distyly is likely due to genic selection against mid‐alleles associated with modified tristylous incompatibility, rather than expression of inbreeding depression.     

基于高通量测序的象山港海域黑鲷(Acanthopagrus schlegelii)食性分析

选取象山港黑鲷个体为研究对象,以18S rDNA为靶标,利用Illumina Miseq高通量测序方法研究黑鲷饵料生物组成特征,分析不同龄组黑鲷的食性异同。通过序列比对,共在黑鲷胃含物中鉴定出41个属中的62种饵料生物,分属9个门,其中节肢动物门（Arthropoda）、绿藻门（Chlorophyta）和软体动物门（Mollusca）是黑鲷饵料生物的优势组成门类。从饵料生物相对丰度和出现频率上分析,石莼（Ulva lactuca）、熊本牡蛎（Crassostrea sikamea）、胸刺水蚤（Centropages hamatus）、日本蟳（Charybdis japonica）、毛蚶（Scapharca subcrenata）和褐菖鲉（Sebastiscus marmoratus）是黑鲷的优势饵料物种,所占饵料生物总相对丰度的比重达60.90%。相似性分析检验（ANOSIM）结果显示：1至4龄黑鲷个体的饵料生物组成不存在显著性差异。与传统食性分析方法相比,高通量测序法在黑鲷饵料生物检测灵敏性上显现了较为明显的优势,保障黑鲷等重要物种的种群稳定对于该海域具有重要的生态和经济意义。     

Breeding systems and phylogenetic diversity of seed plants along a large‐scale elevational gradient

Aim The factors affecting the distribution of dioecious species have received surprisingly little attention and, as a consequence, are poorly understood. For example, there is a well‐documented negative association between dioecy and latitude, for which we have no candidate mechanisms. Conversely, it has been suggested that the relative proportion of dioecious species should be positively correlated with changes in elevation. Location Costa Rica, Central America. Methods We made use of data on the distribution of 175 seed plant species from a series of plots along a transect in Costa Rica that ranged from 30 to 2600 m a.s.l. to test the prediction that dioecy is correlated with elevation. Specifically, we examined relationships between the proportion of dioecy, at the species and individual levels, and the elevation, species richness, number of individuals, and phylogenetic diversity (PD) of plots. For comparison, we repeated all analyses with monoecious species, which also have unisexual flowers but do not suffer from reduced mate assurance and the seed shadow effect that may be the outcomes of having spatially separated sexes. Results The relative proportions of dioecious species and individuals displayed a unimodal relationship with elevation, both peaking at 750 m a.s.l. In contrast, the relative proportions of monoecious species and individuals displayed negative associations with elevation. In addition, the proportion of dioecious species was significantly positively associated with species richness and with the PD of plots. The proportion of monoecious species was not associated with species richness and was weakly positively associated with the PD of plots. Main conclusions Our results suggest that the selection pressure of elevation on the pollinators and life‐history strategy of dioecious species is much less than expected, and is overshadowed by the as‐yet unexplained correlation of dioecy with species richness. Additional studies of the ecology of cosexual and unisexual (i.e. dioecious and monoecious) species along large environmental gradients are needed.     

Habitat use, diet and roost selection by the Big Brown Bat (Eptesicus fuscus) in North America: a case for conserving an abundant species

Insectivorous bats are integral components of terrestrial ecosystems. Despite this, a growing number of factors causing world‐wide declines in bat populations have been identified. Relatively abundant species are important for bat conservation because of their role in ecosystems and the research opportunities they offer. In addition, species that have been well‐studied present unique opportunities to synthesize information and highlight important areas of focus for conservation and research. This paper focuses on a well‐studied abundant bat, Eptesicus fuscus. I review the relevant literature on habitat use, diet and roost selection by E. fuscus in North America, and highlight important areas of conservation and research for this species, including the effects of roost disturbance, control of economically important insect pests, exposure to pesticides, long‐term monitoring of populations, and the potential consequences of expanding populations. These issues have broad implications for other species and can be used to focus future research and conservation efforts.     

Fruit abortion in the Chihuahuan-Desert endemic cactus <Emphasis Type="Italic">Opuntia microdasys</Emphasis>

Resource and pollen limitation, as well as pollen/ovule incompatibility, have been proposed as causes to explain fruit abortion. To assess whether abortion in Opuntia microdasys was due to resource and/or pollen limitation and could therefore be reversed fruit set and seed set were studied using controlled pollination experiments on 60 plants that had been randomly assigned a combination of watering and fertilization treatments. On the other hand, to test whether fruit abortion was irreversible, due to pollen/ovule incompatibility, we examined the reproductive biology of the species. This included observations on floral phenology, nectar production, flower visitors, numbers of pollen grains and ovules, and self-pollination experiments. Results showed that O. microdasys is a fully self-incompatible species and its floral biology and the activity of the main pollinator allow constant deposition of incompatible pollen onto stigmas, which may contribute to fruit abortion. Reproductive success was limited by nutrients and pollen, but the fruit set increased only by 58%, compared to 47% of the control, after the experimental addition of pollen, nutrients and water. The magnitude of pollen and resource limitation suggests that similar levels of abortion will be present in good as well as in bad years. Selfing as well as incompatibility between ramets from the same clone and between closely related plants seem plausible candidates to explain the large proportion of fruit abortion, and experimental cross pollination between genotypes identified through molecular markers are necessary to fully understand the considerable abortion rate that remains unexplained after pollen and resource addition. Interestingly, the possible reason why the abortion of energetically expensive fruits has not been eliminated by natural selection is that the aborted fruits are propagules able to root and produce new plants with the same genotype of the mother. Abortion would have a dramatic effect on cross-fertilized genotypes because they result in zero fitness, but it would have a positive effect on the fitness of the maternal genotype because a clonal offspring is produced. Evidently, the exact fitness consequences to the maternal plant will depend on the differences in survival and reproduction of these different offspring types.     

Do melanin-based tail patterns predict individual quality and sex in Lesser Grey Shrikes Lanius minor ?

In many bird species, males display colourful, usually carotenoid or structurally based plumage ornaments. On the other hand, there are many bird species and entire avian genera that are achromatic, i.e. with predominantly white, grey and black plumage colours. Achromatic plumage is a typical feature in many shrikes for example. In this study, we examine the importance of an achromatic plumage pattern, namely, the black tail spots on the two outermost tail feathers (T6 and T5) of Lesser Grey Shrikes (LGS) for sex discrimination and as an indicator of individual quality. Our results suggest that the black tail patterns, especially spots on T5, are important for sex discrimination, but only in combination with other melanin-based or morphological features. The presence of black tail spots on T5 is also an indicator of male age. However, there is no indication that presence, size and asymmetry of these black spots are indicators of individual quality of both sexes in the terms of breeding performances.     

Aspects of breeding ecology of the eastern olivaceous warbler (Hippolais pallida)

The breeding ecology of eastern olivaceous warblers Hippolais pallida is poorly known. In this study, we provide data on nest site selection and breeding parameters of the species in a population in northwestern Bulgaria, the only one known to be regularly and heavily parasitized by the common cuckoo Cuculus canorus (hereafter cuckoo). Eastern olivaceous warblers only bred within human settlements of the study area, avoiding seemingly suitable habitat outside them. Nests were built in a wide range of plant taxa but ailanthuses Ailanthus altissima and mulberries Morus spp. were most frequently used (21%). After taking into account the availability of vegetation, there was an apparent preference for several plant taxa but not for mulberries. Mean nest height was 1.65 ± 0.98 (0.53–7.60) m, n = 217, and it varied significantly among different types of nesting substrate. Laying date and clutch size of first breeding attempts averaged 10 June ± 0.98 days, n = 101 and 3.9 ± 0.07 (2–5) eggs, n = 72, respectively. Hatching success, fledging success, and breeding success were 42.5, 86.4, and 36.7%, respectively. The main sources of nest mortality were predation and cuckoo parasitism, with no significant difference in the proportion of nests lost to each. Cuckoo parasitism seemed responsible for the relatively low hatching success in this population.     

Manipulation of laying effort reveals habitat-specific variation in egg production constraints in Great Tits (Parus major)

It has been suggested that a bird's clutch size is not limited by the amount of resources available at the time of laying but that differences in the availability of food for nestlings is the ultimate underlying factor determining spatio-temporal variations in clutch size. However, habitat-related variations in egg production ability has yet to be investigated explicitly. We studied the breeding of Great Tits Parus major in deciduous and coniferous forests in the same area. The sizes of both the clutches and the eggs were, on average, larger in the former habitat than in the latter. A number of females were induced to lay more eggs than usual by removing four eggs from designated experimental clutches early in the laying period. These manipulated females laid approximately one egg more than control females, with the number of additional eggs laid not differing between the habitats. However, in both study years the relative size of the extra eggs – relative to the mean size of earlier laid eggs of the same clutch – was smaller in the coniferous habitat than in the deciduous habitat, while there was no habitat-related difference in the relative size of the last-laid eggs of control clutches. This result indicates that some form of proximate limitation during egg-laying period can contribute to the relatively small clutches and eggs in the coniferous habitat. Our results emphasize the need to take egg production costs into account when attempting to account for spatial variation in the reproductive behaviour of birds.     

Spatiotemporal variation in reproductive parameters of yellow-bellied marmots

Spatiotemporal variation in reproductive rates is a common phenomenon in many wildlife populations, but the population dynamic consequences of spatial and temporal variability in different components of reproduction remain poorly understood. We used 43 years (1962–2004) of data from 17 locations and a capture–mark–recapture (CMR) modeling framework to investigate the spatiotemporal variation in reproductive parameters of yellow-bellied marmots (Marmota flaviventris), and its influence on the realized population growth rate. Specifically, we estimated and modeled breeding probabilities of two-year-old females (earliest age of first reproduction), >2-year-old females that have not reproduced before (subadults), and >2-year-old females that have reproduced before (adults), as well as the litter sizes of two-year old and >2-year-old females. Most reproductive parameters exhibited spatial and/or temporal variation. However, reproductive parameters differed with respect to their relative influence on the realized population growth rate (λ). Litter size had a stronger influence than did breeding probabilities on both spatial and temporal variations in λ. Our analysis indicated that λ was proportionately more sensitive to survival than recruitment. However, the annual fluctuation in litter size, abetted by the breeding probabilities, accounted for most of the temporal variation in λ. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.