The complex history of the domestication of rice

BACKGROUND: Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. SCOPE: Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. CONCLUSIONS: The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.     

Honey bees can disseminate a microbial control agent to more than one inflorescence pest of oilseed rape

Pollen beetles (Meligethes aeneus) and cabbage seed weevils (Ceutorhynchus assimilis) are major pests of oilseed rape (Brassica napus) throughout Europe. In field cage experiments in both winter and spring rape, honey bees (Apis mellifera) effectively transported the entomopathogenic fungus Metarhizium anisopliae to the flowers, causing infection and mortality of both adult and larval pollen beetles, as well as of adult seed weevils. External conidiation was observed on many of the dead pest insects. Although some external conidiation also occurred on dead honey bees, reduction in honey bee colony size during the experiments appeared unrelated to the fungus. The potential of this technique for integration into pest management strategies for the crop, particularly in association with a trap crop, is discussed.     

云南红河和保山两地区小蜜蜂巢房结构比较研究

【目的】本研究旨在对自然环境条件明显不同的云南红河和保山两地区小蜜蜂Apis florea巢房结构进行量化分析,以期揭示这两个地区间小蜜蜂巢房结构的差异性。【方法】测量小蜜蜂子脾厚度、小蜜蜂巢脾上连续10个工蜂巢房的宽度;利用环氧树脂填充巢房,制作巢房模型,基于巢房模型比较两地区小蜜蜂工蜂和雄蜂单个巢房直径、口部边长、棱长、深度和容积及巢房倾斜角的差异。【结果】云南 红河地区小蜜蜂工蜂、雄蜂子脾厚度均极显著小于保山地区的。两地区小蜜蜂连续10个工蜂巢房的宽度在0°方向均显著大于60°和120°方向的宽度,60°和120°方向的宽度之间差异均不显著,两地区小蜜蜂工蜂单个巢房直径在3个方向上也表现出显著差异, 而两地区雄蜂单个巢房的直径在3个方向上均没有显著性差异。红河地区小蜜蜂工蜂巢房直径在3个方向上均显著小于保山地区的,而两地区小蜜蜂雄蜂巢房直径在3个方向上均差异不显著。红河地区小蜜蜂工蜂、雄蜂单个巢房口部边长、棱长、深度和容积均极显著小于保山地区的;两地区工蜂巢房的倾斜角差异不显著。【结论】小蜜蜂巢房的结构存在地区性差异,海拔高、温度低的地区小蜜蜂巢房结构尺寸明显大于海拔低、温度高地区的。本研究结果不仅丰富了小蜜蜂的生物学知识,也为后续研究小蜜蜂巢房结构指标与形态学指标关联性研究提供了思路。     

Multiple host shifts by the emerging honeybee parasite,Varroa jacobsoni

Host shifts are a key mechanism of parasite evolution and responsible for the emergence of many economically important pathogens. Varroa destructor has been a major factor in global honeybee (Apis mellifera) declines since shifting hosts from the Asian honeybee (Apis cerana) > 50 years ago. Until recently, only two haplotypes of V. destructor (Korea and Japan) had successfully host shifted to A. mellifera. In 2008, the sister species V. jacobsoni was found for the first time parasitizing A. mellifera in Papua New Guinea (PNG). This recent host shift presents a serious threat to world apiculture but also provides the opportunity to examine host shifting in this system. We used 12 microsatellites to compare genetic variation of V. jacobsoni on A. mellifera in PNG with mites on A. cerana in both PNG and surrounding regions. We identified two distinct lineages of V. jacobsoni reproducing on A. mellifera in PNG. Our analysis indicated independent host shift events have occurred through small numbers of mites shifting from local A. cerana populations. Additional lineages were found in the neighbouring Papua and Solomon Islands that had partially host shifted to A. mellifera, that is producing immature offspring on drone brood only. These mites were likely in transition to full colonization of A. mellifera. Significant population structure between mites on the different hosts suggested host shifted V. jacobsoni populations may not still reproduce on A. cerana, although limited gene flow may exist. Our studies provide further insight into parasite host shift evolution and help characterize this new Varroa mite threat to A. mellifera worldwide.     

Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools

Background

With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F_ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions.

Results

We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.

Conclusions

These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows (http://usegalaxy.org/r/kenyanbee) that can be applied to any model system with genomic information.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1712-0) contains supplementary material, which is available to authorized users.     

Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern‐East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.     

Natural and within-farmland biodiversity enhances crop productivity

Ongoing expansion of large-scale agriculture critically threatens natural habitats and the pollination services they offer. Creating patches with high plant diversity within farmland is commonly suggested as a measure to benefit pollinators. However, farmers rarely adopt such practice, instead removing naturally occurring plants (weeds). By combining pollinator exclusion experiments with analysis of honeybee behaviour and flower-visitation webs, we found that the presence of weeds allowed pollinators to persist within sunflower fields, maximizing the benefits of the remaining patches of natural habitat to productivity of this large-scale crop. Weed diversity increased flower visitor diversity, hence ameliorating the measured negative effects of isolation from natural habitat. Although honeybees were the most abundant visitors, diversity of flower visitors enhanced honeybee movement, being the main factor influencing productivity. Conservation of natural patches combined with promoting flowering plants within crops can maximize productivity and, therefore, reduce the need for cropland expansion, contributing towards sustainable agriculture.