Genomic analyses of modern dog breeds

A rose may be a rose by any other name, but when you call a dog a poodle it becomes a very different animal than if you call it a bulldog. Both the poodle and the bulldog are examples of dog breeds of which there are >400 recognized worldwide. Breed creation has played a significant role in shaping the modern dog from the length of his leg to the cadence of his bark. The selection and line-breeding required to maintain a breed has also reshaped the genome of the dog, resulting in a unique genetic pattern for each breed. The breed-based population structure combined with extensive morphologic variation and shared human environments have made the dog a popular model for mapping both simple and complex traits and diseases. In order to obtain the most benefit from the dog as a genetic system, it is necessary to understand the effect structured breeding has had on the genome of the species. That is best achieved by looking at genomic analyses of the breeds, their histories, and their relationships to each other.     

航天与辐射共诱变在水稻育种中的应用

利用航天诱变与辐射诱变相结合的方法进行水稻新种质、新品种的选育,显著地提高其突变频率和突变类型,提高诱变育种的选择效果,育成1个两系杂交水稻新组合“培两优721”及一批优质水稻新种质和新品系(组合)。     

Oceanography and Marine Environment of the Basque Country. Elsevier Oceanography Series 70. Edited by A. Borja and M. Collins (2004) Elsevier B.V., Amsterdam. ISBN 0-444-51581-X. ISSN 0422-9894 (Series).

This is not a book that you probably start reading from thefirst page. Its 24 review chapters have informative titles andare organised in seven sections that together with a four-pagelocation index and an eight-page subject index invites you todive for your favourite subjects. The editors have succeededto structure the book in ways that makes easy navigation amongstits     

Tracing the genetic roots of the indigenous White Park Cattle

The White Park Cattle (WPC) is an indigenous ancient breed from the British Isles which has a long‐standing history in heroic sagas and documents. The WPC has retained many primitive traits, especially in their grazing behaviour and preferences. Altogether, the aura of this breed has led to much speculation surrounding its origin. In this study, we sequenced the mitogenomes from 27 WPC and three intronic fragments of genes from the Y chromosome of three bulls. We observed six novel mitogenomic lineages that have not been found in any other cattle breed so far. We found no evidence that the WPC is a descendant of a particular North or West European branch of aurochs. The WPC mitogenomes are grouped in the T3 cluster together with most other domestic breeds. Nevertheless, both molecular markers support the primitive position of the WPC within the taurine breeds.     

Marker-derived phylogeny of European cattle supports demic expansion of agriculture

Using frequencies of 86 genes from 23 loci of blood group systems, blood and milk proteins, the genetic relationships among 14 cattle breeds including four native Balkan and four synthetic Balkan-Alp breeds were studied. The dendrogram and nonlinear map construction shows a consensus ‘Balkan breed cluster’, an ‘Alp breed cluster’, an unstable position of synthetic breeds and well-separated American breeds. Positive partial correlations between genetic distance and time elapsed since introduction of farming while keeping geographical distances constant, and regular patterns over thousands of kilometres indicate that large-scale cattle population movements together with human migration (in the Neolithic age) from the Near East into Europe across the Balkans are the most likely explanation for the genetic distances observed in our data. More recent breed differentiation and selection do not yet blur this initial pattern of European cattle populations.     

The distribution of pathotypes of the cereal cyst-eelworm Heterodera avenae in England and Wales

Two pathotypes of the cereal cyst-eelworm (Heterodera avenae), occurred commonly in England and Wales and a third pathotype was apparently present in low numbers in a few areas. Pathotype 1, which can breed on most cultivars of wheat, barley and oats, but not on Drost barley nor barley cultivars containing the gene for resistance from barley No. 191, was most common in the south west of England. Pathotype 2, which can breed on most cereals, including Drost barley but not No. 191, was common throughout England and Wales and mixtures of these pathotypes occurred in many places. Pathotype 3, which can breed on barley No. 191 and probably on Drost and most cultivars of cereals, was rare and was found only in low numbers together with either or both Pathotypes 1 and 2. In the initial tests it was present or suspected in only nine fields (6%), but when these soils were retested in more detail the following year, Pathotype 3 was confirmed at only one site.     

Sex differences in the drivers of reproductive skew in a cooperative breeder

Many cooperatively breeding societies are characterized by high reproductive skew, such that some socially dominant individuals breed, while socially subordinate individuals provide help. Inbreeding avoidance serves as a source of reproductive skew in many high‐skew societies, but few empirical studies have examined sources of skew operating alongside inbreeding avoidance or compared individual attempts to reproduce (reproductive competition) with individual reproductive success. Here, we use long‐term genetic and observational data to examine factors affecting reproductive skew in the high‐skew cooperatively breeding southern pied babbler (Turdoides bicolor). When subordinates can breed, skew remains high, suggesting factors additional to inbreeding avoidance drive skew. Subordinate females are more likely to compete to breed when older or when ecological constraints on dispersal are high, but heavy subordinate females are more likely to successfully breed. Subordinate males are more likely to compete when they are older, during high ecological constraints, or when they are related to the dominant male, but only the presence of within‐group unrelated subordinate females predicts subordinate male breeding success. Reproductive skew is not driven by reproductive effort, but by forces such as intrinsic physical limitations and intrasexual conflict (for females) or female mate choice, male mate‐guarding and potentially reproductive restraint (for males). Ecological conditions or “outside options” affect the occurrence of reproductive conflict, supporting predictions of recent synthetic skew models. Inbreeding avoidance together with competition for access to reproduction may generate high skew in animal societies, and disparate processes may be operating to maintain male vs. female reproductive skew in the same species.     

THE UTILIZATION OF GUM TREES BY BIRDS IN AFRICA

The changes brought about by the introduction of Eucalyptus into Africa on the ecology of birds are outlined, in so far as its contribution as a habitat, as a food-source, and for other uses is concerned. Species known to breed in gums are listed, together with notes on habitat preference, and its limitations in comparison with the indigenous resources are discussed.     

Breed demarcation and potential for breed allocation of horses assessed by microsatellite markers

Population demarcation of eight horse breeds was investigated using genotype information of 306 horses from 26 microsatellite loci. The breeds include the indigenous Norwegian breeds Fjord Horse, Nordland/Lyngen Horse, Døle Horse and Coldblooded Trotter together with Icelandic Horse, Shetland Pony, Standardbred and Thoroughbred. Both phylogenetic analysis and a maximum likelihood method were applied to examine the potential for breed allocation of individual animals. The phylogenetic analysis utilizing simple allele sharing statistics revealed clear demarcation among the breeds; 95% of the individuals clustered together with animals of the same breed in the phylogenetic tree. Even breeds with a short history of divergence like Døle Horse and Coldblooded Trotter formed distinct clusters. Implementing the maximum likelihood method allocated 96% of the individuals to their source population, applying an assignment stringency of a log of the odds ratio larger than 2. Lower allocation stringency assigned nearly all the horses. Only three individuals were wrongly allocated a breed by both methods. In conclusion, the study demonstrates clear distinction among horse breeds, and by combining the two assignment methods breed allocation could be determined for more than 99% of the individuals.     

From irreversible thermodynamics to network thermodynamics

Whenever the subject of the thermodynamics of irreversible processes TIP is brought up among biologists, there seems to be a very polarized reaction: some have found it a useful tool, others reject it utterly, and for some reason which I do not understand, even fervently. For the present school, Professor Aharon Katchalsky had suggested that we try together to point out some ways in which TIP has been useful, to discuss limitations and shortcomings, and, finally, to show the direction and first results of present efforts, mainly in network thermodynamics¹. It would have been my task to show you the darker side of the coin, but now Aharon is not with us to show you the shining side in his unique way, to carry you along with his enthusiasm. I believe it is in Aharon's spirit that I do not attempt to evaluate or commemorate his contributions and achievements, but just talk science and try to convey a little of what was at the center of his interest during the last years.     

Inbreeding and genetic structure in the endangered Sorraia horse breed: implications for its conservation and management

The Sorraia horse is a closed breed with reduced effective population size and considered in critical maintained risk status. The breed exists in 2 main breeding populations, one in Portugal and one in Germany, with a smaller population size. A set of 22 microsatellite loci was used to examine genetic diversity and structure of the Sorraia horse breed and to compare individual inbreeding coefficient F, estimated from pedigree data, with individual heterozygosity and mean d(2). The Sorraia horse shows lower levels of microsatellite diversity when compared with other horse breeds. Due to management strategies, there are clear differences in the genetic structure of the 2 main Sorraia horse populations. Individual heterozygosity was shown to be a good estimator, used together with or as an alternative to inbreeding coefficient, in predicting fitness and evaluating the inbreeding level of the Sorraia horse. The information gathered in this study, combined with information available from previous studies, offers an important and wide information base for the future development of an effective breeding management of the Sorraia horse in order to preserve this endangered breed.     

Some aspects of social behaviour in domestic sheep

Aspects of social behaviour in domestic sheep were studied by observations of undisturbed flocks. A group identity was found to develop when small flocks are established: when two such groups of similar age and sex are amalgamated, random mixing takes up to 3 weeks to develop. Breed identity was also found to exist: within flocks made up from groups of sheep of different breeds, the sheep had a strong bias for associating with others of their own breed both whilst grazing and whilst camping, and this remains even after 2 years of grazing together. This breed identity remained in the offspring born into a flock of ewes of different breeds.     

Finding autophagy

To tell the truth, I find it difficult to work when flying, or even when sitting in an airport for an extended period of time. So, typically I take along a book to read. And when I truly cannot concentrate, for example when a flight is considerably delayed, I have even been known to resort to word puzzles. Depending on the type, they do not require much attention (that is, you can pick up right where you left off after you glance at the flight status screen for the twentieth or so time, even though you know nothing has changed), or effort (although you need to use a pen or pencil, not a keyboard), but nonetheless they can keep your mind somewhat occupied. I even rationalize doing them based on the assumption that they are sharpening my observational/pattern-finding skills. One type of word puzzle that is particularly mindless, but for that very reason I still enjoy in the above circumstances, is a word search; you are given a grid with letters and/or numbers, and a list of “hidden” terms, and you circle them within the grid, crossing them off the list as you go along. I do admit that the categories of terms used in the typical word searches can become rather mundane (breeds of dog, types of food, words that are followed by “stone,” words associated with a famous movie star, words from a particular television show, etc.). Therefore, on one of my last seminar trips I decided to generate my own word search, using the category of autophagy.     

基于WWW的生物信息集成检索系统的研制

生物信息检索和获取成为当前非常重要而紧迫的研究课题,我们采用元搜索引擎技术、JAVA和HTML编程语言研制开发了基于WWW生物信息集成检索系统,该系统提供了统一的检索界面,对15分子生物学数据库和3个通用搜索引擎实现多功能、复合型、全开放的集成检索。该系统为广大从事医学、分子生物学、分子肿瘤学、分子遗传学以度人类基因组的科研人员准确、及时、综合获取多种生物信息资源,具有极为重要而深远的意义。     

Genetic variability,structure and assignment of Spanish and French pig populations based on a large sampling

The Spanish and French pig populations share the common practice of quasi systematic paternity control of pure breed and composite line males. Ten microsatellite markers are in common between Spain and France controls, among the 17 markers used in France and the 13 used in Spain. After the adjustment of allele sizes, it is possible to merge the two datasets and to obtain a set of 5791 animals, including the vast majority of the males in the Duroc, Landrace, Large White and Piétrain French and Spanish breeds. Twelve French composite lines are also available. The genetic diversity analysis of these pig populations is presented, as well as the assignment of an individual to its breed. The effects of heterogeneous sampling across time and of relatedness among animals are also assessed. Consistent with the results of the previous studies, we found that different populations from the same breed clearly clustered together. In addition, all populations of this study, whether purebred or composite, are quite well differentiated from the other ones. As a result, we note that the 10 microsatellites commonly used for paternity control ensure a powerful detection of the breed of origin, with the power of detection being 95–99%. The detection of the exact population within breed is more difficult, but the power exceeds 70% for most of the populations. Practical implications include, for instance, the detection of outlier animals, crosses and admixture events.     

Diet flexibility in a declining long‐distance migrant may allow it to escape the consequences of phenological mismatch with its caterpillar food supply

Climate‐driven shifts in prey phenology may lead to asynchrony with the timing of peak resource requirements of their predators, leading to a reduction in productivity and population declines. Migrant species that cannot adjust their arrival times may be particularly at risk, especially those that breed in seasonal environments and for which a temporarily super‐abundant prey source is important, such as insectivorous passerine birds that take advantage of the seasonal flush of caterpillars to feed their young. We assess whether population declines of the trans‐Saharan migratory Wood Warbler Phylloscopus sibilatrix are likely to have been caused by phenological mismatch. We measured seasonal invertebrate biomass and various fitness parameters, including the timing of breeding and breeding success, in two time periods: 1982–1984, prior to the species’ decline in the UK, and 2009–2011, as the reduction in numbers continued. Although birds bred on average a week earlier in 2009–2011 than in 1982–1984, this was not adequate to track the more rapid advancement of peak caterpillar biomass, which advanced by 12 days and was closely correlated with spring temperatures. Moreover, although caterpillars were the dominant prey fed to nestlings, there was only limited evidence that productivity was positively related to caterpillar biomass in the environment. Considering only successful nests, synchrony with the food peak did not produce heavier nestlings and had only a small positive effect on fledging success, although there was a seasonal decline in productivity when all nests were considered. We conclude that the lack of a marked effect of the observed mismatch is due to Wood Warblers’ generalist diet, enabling them to breed successfully on prey other than caterpillars. Although other studies have demonstrated that climate‐driven asynchrony of predator and prey populations can have impacts on avian demography, this study highlights the importance of investigating the generality of those findings.     

Finding autophagy: It’s a question of how you look at it

To tell the truth, I find it difficult to work when flying, or even when sitting in an airport for an extended period of time. So, typically I take along a book to read. And when I truly cannot concentrate, for example when a flight is considerably delayed, I have even been known to resort to word puzzles. Depending on the type, they do not require much attention (that is, you can pick up right where you left off after you glance at the flight status screen for the twentieth or so time, even though you know nothing has changed), or effort (although you need to use a pen or pencil, not a keyboard), but nonetheless they can keep your mind somewhat occupied. I even rationalize doing them based on the assumption that they are sharpening my observational/pattern-finding skills. One type of word puzzle that is particularly mindless, but for that very reason I still enjoy in the above circumstances, is a word search; you are given a grid with letters and/or numbers, and a list of “hidden” terms, and you circle them within the grid, crossing them off the list as you go along. I do admit that the categories of terms used in the typical word searches can become rather mundane (breeds of dog, types of food, words that are followed by “stone,” words associated with a famous movie star, words from a particular television show, etc.). Therefore, on one of my last seminar trips I decided to generate my own word search, using the category of autophagy.     

Human voice perception

We are all voice experts. First and foremost, we can produce and understand speech, and this makes us a unique species. But in addition to speech perception, we routinely extract from voices a wealth of socially-relevant information in what constitutes a more primitive, and probably more universal, non-linguistic mode of communication. Consider the following example: you are sitting in a plane, and you can hear a conversation in a foreign language in the row behind you. You do not see the speakers' faces, and you cannot understand the speech content because you do not know the language. Yet, an amazing amount of information is available to you. You can evaluate the physical characteristics of the different protagonists, including their gender, approximate age and size, and associate an identity to the different voices. You can form a good idea of the different speaker's mood and affective state, as well as more subtle cues as the perceived attractiveness or dominance of the protagonists. In brief, you can form a fairly detailed picture of the type of social interaction unfolding, which a brief glance backwards can on the occasion help refine - sometimes surprisingly so. What are the acoustical cues that carry these different types of vocal information? How does our brain process and analyse this information? Here we briefly review an emerging field and the main tools used in voice perception research.     

A patient's guide to choosing unconventional therapies

Unconventional therapies (UTs) are therapies not usually provided by Canadian physicians or other conventionally trained health care providers. Examples of common UTs available in Canada are herbal preparations, reflexology, acupuncture and traditional Chinese medicine. UTs may be used along with conventional therapies (complementary) or instead of conventional therapies (alternative). Surveys have shown that many Canadians use UTs, usually as complementary therapies, for a wide range of diseases and conditions. Reliable information about UTs is often difficult to find. Your doctor may be unable to give you specific advice or recommendations, since UTs are often not in a physician''s area of expertise. However, he or she will usually be able to provide some general advice and help supervise your progress. For your own health and safety, it is important to keep your doctor informed of the choices you make. This document is intended to (a) provide you with questions to consider when making your treatment choices, (b) help you find information about UTs, (c) help you decide whether a specific UT is right for you, and (d) provide tips to help you evaluate the information you find.     

Analysis of single nucleotide polymorphisms variation associated with important economic and computed tomography measured traits in Texel sheep

Sheep are an important part of the global agricultural economy. Growth and meat production traits are significant economic traits in sheep. The Texel breed is the most popular terminal sire breed in the UK, mainly selected for muscle growth and lean carcasses. This is a study based on a genome-wide association approach that investigates the links between some economically important traits, including computed tomography (CT) measurements, and molecular polymorphisms in UK Texel sheep. Our main aim was to identify single nucleotide polymorphisms (SNP) associated with growth, carcass, health and welfare traits of the Texel sheep breed. This study used data from 384 Texel rams. Data comprised ten traits, including two CT measured traits. The phenotypic data were placed in four categories: growth traits, carcass traits, health traits and welfare traits. De-regressed estimated breeding values (EBV) for these traits together with sire genotypes derived with the Ovine 50 K SNP array of Illumina were jointly analysed in a genome wide association analysis. Eight novel chromosome-wise significant associations were found for carcass, growth, health and welfare traits. Three significant markers were intronic variants and the remainder intergenic variants. This study is a first step to search for genomic regions controlling CT-based productivity traits related to body and carcass composition in a terminal sire sheep breed using a 50 K SNP genome-wide array. Results are important for the further development of strategies to identify causal variants associated with CT measures and other commercial traits in sheep. Independent studies are needed to confirm these results and identify candidate genes for the studied traits.