岁立云本周报告内容：Efficiency of selection, as measured by single nucleotide polymorphism variation, is dependent on inbreeding rate in Drosophila melanogaster

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刘伟本周报告内容：Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits

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欢迎大家提前观看。

相关文章见下载链接：
1.statistical methods in spatial genetics
2.SM of statistical methods in spatial genetics
3.He Ruikun's paper

李大卫本周报告内容：hybridzation and speciation

李文彬本周的Journal Club 报告，下一代测序技术介绍。

Sun Wei's PPT in last Journal club (10.29). Please download it quickly in one month. It is a version with lower resolution. If you want a higher resolution of the PPT images,please contact me or the speaker.

Click here for downloading!

Hybridization in plants and animals is more common and has more complex outcomes than previously realized. Genomewide analyses of introgression in organisms ranging from oaks to sunflowers to fruit flies show that a substantial fraction of their genomes are permeable to alleles from related species. Hybridization can lead to rapid genomic changes, including chromosomal rearrangements, genome expansion, differential gene expression, and gene silencing, some of which are mediated by transposable elements. These genomic changes may lead to beneficial new phenotypes, and selection for fertility and ecological traits may in turn alter genome structure. Dramatic increases in the availability of genomic tools will produce a new understanding of the genetic nature of species and will resolve a century-old debate over the basis of hybrid
vigor, while the natural recombinants found in hybrid zones will permit genetic mapping of species differences and reproductive barriers in nonmodel organisms.

I have shared my Google reader items here:My Google reader sharing itemsWelcome to visit it.

Species that are habitat specialists make up much of biodiversity, but the evolutionary factors that limit their distributions have rarely been considered. We show that in Drosophila, narrow and wide ranges of desiccation and cold resistance are closely associated with the distributions of specialist and generalist species, respectively. Furthermore, our data show that narrowly distributed tropical species consistently have low means and low genetic variation for these traits as compared with those
of widely distributed species after phylogenetic correction. These results are unrelated to levels of neutral variation. Thus, specialist species may simply lack genetic variation in key traits, limiting their ability to adapt to conditions beyond their current range. We predict that such species are likely to be constrained in their evolutionary responses to future climate changes.

上帝和进化论真的誓不两立吗？人们总有办法调解。

long distance disperse不是新的理论，进来由于分子钟的应用这一理论被用来解释许多类群的分布格局的形成，但是这毕竟是间接的推断，长距离传播的直接证据毫无疑问是十分重要的，Ran非常热衷于长距离传播理论，在这综述中总结了主要的一些传播途径，不妨一读。

如题，这是一个很普遍的现象，但是好像没有量化的标准，Michael Cummings在这篇文章中针对这一问题描述一个比较容易理解的模型以及相应的软件。可能意义不是特别大，比如不能回答居群变化历史等具体问题，不管怎样没事的时候不妨把玩把玩。
另外Michael实在太帅了，超像巴乔。

Molecular evolution of PISTILLATA-like genes
in the dogwood genus Cornus (Cornaceae)

Molecular phylogenetics and evolution

Please tell me the journal and title link. <img src="http://bbs.niuhuifei.com/bb-plugins/bb-smilies/default/icon_rolleyes.gif" title=":roll:" class="bb_smilies" />

一篇刚刚在我们实验室做过报告的向博士实验室的文章。
Abstract
应用MADS-box转录因子的B类基因PI-LIKE基因来揭示四照花属中PI基因的进化历史。
为什么要选择这类基因呢？文中给出答案是，因为在四照花属中Petaloid bract即花瓣状苞片是该属最大的亮点，同时也是却别属下分类的好的性状之一。

Result and conclusion
1.一次古老的Duplicaion使得在四照花产生了CorPI-A and CorPI-B
2.。。。。。。。。后边就自己看吧

没有人认为分子系统学是完美无缺的，经过三十年左右的发展，除了看到这一研究工具的诸多优点，也的确是时候注意其中可能存在的问题了，尽管诸如基因树，物种树，基因复制重组等等问题一直以来就有人提起。

可以预见，基因组研究很快可以运用到模式生物以外的研究体系中来，技术的革新才是推动学科发展的关键。

A smart idea and excellent work. I'd like to extend this topic with one more paper on PNAS or somewhere else. I will attach it later.

和进化相比，生物地理的研究以及相关的分析方法都要少得多。当一个分类学家第一眼看到一个类群，他可能首先想到的是性状的进化。其实生物地理分布的“进化”也构成了复杂丰富的生物体进化历史的一部分，而且也给进化生物学家许多灵感，要不是环球航行的经历，也许有关生物进化的灵感就不会闪过达尔文的天才大脑也难说。如果你是达尔文，在你到达加拉帕格斯群岛的时候，也许也会对这些小岛上的生物和大陆的生物之间的差异感到惊异不已，除了环境也许稍有差异，它们之间不同的只是一个在大陆，一个隔离在小岛，地理隔离理所当然会成为解释这一差异的首要选项，因为不论是在南美大陆还是在太平洋小岛，上帝都是同一个，不是吗？
到目前为止，用于生物地理学分析的方法少之又少。还健在的老一辈植物地理学家的观点大多深受板块飘逸学说的影响，如我国的吴先生和Peter Raven等，他们无疑是伟大的学者，但是许多观点恐怕还是要依靠技术的发展让最新的数据来说话，而不是一看到一个洲际间断比如一个在南美，另一个姐妹群一个在非洲就认为是冈瓦纳古陆起源而后由于板块分离后隔离分化的孑遗。
还是回到Rich的这篇文章，这应该是理解生物地理分布区expansion, extiction,plant speciation的一个非常好的开端。以往的一些分析，比如dispersal-vicariance(DIVA)分析，基于一个没有任何parameter的系统树以及现有分布区，利用简约原则推到可能的起源和扩散方式，但是真实的物种进化历史上又怎么可能是这样的一种情况？
不可否认的是，range analysis还是受到信息量的限制。实在没有办法，有的问题是注定不能够在今天得到完美解答的，最终恐怕还是要依靠技术上的革命。
另,上传的文件大小限制有点让人头痛......

Sotlis实验室可以说是现在做population genetics和Phyloeny最牛的实验室了，当然他们实验室对物种形成机制也做了大量的工作。（似乎刘师兄已经把他们的新Reviews放上去了）我来Upload一篇关于花部进化的文章，这也是他们实验室最近在开展的工作。
如果你对被子植物的花部基因组学很感兴趣的话，嘿嘿，就Download下来看看哦。我把这篇文章的亮点说说，
由于这篇文章是对Basal lineage of angiosperm的系统进化进行综述，
他首先介绍了最近的最基部被子植物分子系统学的研究进展，互叶梅科Amorella是现存所有被子植物首先分化出来的，Austrobaileyales木兰藤目和Nymphaeales睡莲目紧跟其后（说道这里我想起了，武汉园还把八角定义为木兰科的呢，我晕死在大街上）。值得注意的是金粟兰科Chloranthaceae和木兰一支随后分出。再接下来才是单子叶植物，之后才是备受争议的金鱼藻呢。当然金鱼藻就成了Eudicot最近的亲戚啦。
再看花部进化这块，主要分为了数目，大小；花被片进化；以及对称性进化三部分进行阐述的。基部被子植物花部为什么形态那么多样呢？他总结就是这几个原因吧。
我们单拿他的子标题看看，都讲了哪些热点。（这个可是以后搞分类和进化的都想去趟点“浑水”的方向哦）
1.ABCE模型在基部被子植物的应用来解释花部的多样
2 CYCLOIDEA和other genes控制对称性的，这段好好看看，挺有启发的。
3 就是一些其他基因控制花型的了
现在在中国开展EVO-DEVO的科学家还不是很多，仅有的几个也是专注于自己感兴趣的类群。就像每个人瓜分一样，互补侵犯。真有意思。
我来说说，罗达老师很牛，Cell杂志发表了他通过金鱼草对称性的突破性研究。之后他一直对豆科的花部对称性很感兴趣。
孔宏智老师，做金粟兰起家的，没想到这个科的位置那么特别，之后就继续做下去了，现在主要做 Ranulanceae的花部进化
贺超英老师（男），做Solanaceae一些非常特别NOVEL花器官的发育
孟征老师，做花发育的专家，现在为什么对太行花那么感兴趣？
王印政老师：苦苣苔科专家，开始做了这个类群的对称性研究，文章的档次大大大大的提高了。
当然还有很多老师想涉猎这个领域呢，被子植物的进化就是intriguing and mystical。

Joshua（巨帅)还没有完全都的很详细，今天我要把这篇文章啃透。

第一时间得到这么新的文献资料 :D谢谢！

Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella , the putative sister species to other extant angiosperms. The question is no longer “ What proportion of angiosperms are polyploid? ” , but “ How many episodes
of polyploidy characterize any given lineage? ” New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversifi cation rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.

Soltis实验室出品

I examined the potential influence of climate change on the dynamics of a previously studied hybrid zone between a pair of terrestrial salamanders at the Coweeta Hydrologic Laboratory, U.S. Forest Service, in the Nantahala Mountains of North Carolina, USA. A 16-year study led by Nelson G. Hairston, Sr. revealed that Plethodon teyahalee and Plethodon shermani hybridized at intermediate elevations, forming a cline between 'pure' parental P. teyahalee at lower elevations and 'pure' parental P. shermani at higher elevations. From 1974 to 1990 the proportion of salamanders at the higher elevation scored as 'pure'P. shermani declined significantly, indicating that the hybrid zone was spreading upward. To date there have been no rigorous tests of hypotheses for the movement of this hybrid zone. Using temperature and precipitation data from Coweeta, I re-analyzed Hairston's data to examine whether the observed elevational shift was correlated with variation in either air temperature or precipitation from the same time period. For temperature, my analysis tracked the results of the original study: the proportion of 'pure'P. shermani at the higher elevation declined significantly with increasing mean annual temperature, whereas the proportion of 'pure'P. teyahalee at lower elevations did not. There was no discernable relationship between proportions of 'pure' individuals of either species with variation in precipitation. From 1974 to 1990, low-elevation air temperatures at the Coweeta Laboratory ranged from annual means of 11.8 to 14.2 °C, compared with a 55-year average (1936–1990) of 12.6 °C. My re-analyses indicate that the upward spread of the hybrid zone is correlated with increasing air temperatures, but not precipitation, and provide an empirical test of a hypothesis for one factor that may have influenced this movement. My results aid in understanding the potential impact that climate change may have on the ecology and evolution of terrestrial salamanders in montane regions.

Web link

还是不太明白。 <img src="http://bbs.niuhuifei.com/bb-plugins/bb-smilies/default/icon_question.gif" title=":?:" class="bb_smilies" />

值得一读，PDF奉上。

没有搞懂，这样的推论到底和真实的情节有什么差异。没有人可以真正的证明其对错，因为没有人可以还原现场。 <img src="http://bbs.niuhuifei.com/bb-plugins/bb-smilies/default/icon_question.gif" title=":?:" class="bb_smilies" />

当人将他们驯化后又开始研究人是怎么驯化的，很奇妙的科学研究。 <img src="http://bbs.niuhuifei.com/bb-plugins/bb-smilies/default/icon_rolleyes.gif" title=":roll:" class="bb_smilies" />

亚洲类似的地方可能就是中国的西部山区。很多类似的研究，但没有一般性的结论。

just a test for reply <img src="http://bbs.niuhuifei.com/bb-plugins/bb-smilies/default/icon_redface.gif" title=":oops:" class="bb_smilies" />

Journal club
From Wikipedia, the free encyclopedia

A journal club is a group of individuals who meet regularly to critically evaluate recent articles in scientific literature. Journal clubs are usually organized around a defined subject in basic or applied research. For example, the application of evidence-based medicine to some area of medical practice can be facilitated by a journal club. Typically, each participant can voice their view relating to several questions such as the appropriateness of the research design, the statistics employed, the appropriateness of the controls that were used, etc. There might be an attempt to synthesize together the results of several papers, even if some of these results might first appear to contradict each other. Even if the results of the study are seen as valid, there might be a discussion of how useful the results are and if these results might lead to new research or to new applications.

Journal clubs are sometimes used in the education of graduate or professional students. These help make the student become more familiar with the advanced literature in their new field of study. In addition, these journal clubs help improve the students' skills of understanding and debating current topics of active interest in their field. This type of journal club may sometimes be taken for credit. Research laboratories may also organize journal clubs for all researchers in the lab to help them keep up with the literature produced by others who work in their field.

History

The earliest references to a journal club is found in a book of memoirs and letters by the late Sir James Paget, a British surgeon, who describes a group at St. Bartholomew's Hospital in London in the mid-1800s as "a kind of club ... a small room over a baker's shop near the Hospital-gate where we could sit and read the journals."

Sir William Osler established the first formalized journal club at McGill University in Montreal in 1875. The original purpose of Osler's journal club was "for the purchase and distribution of periodicals to which he could ill afford to subscribe."

Evolutionary biologists often wish to explore the impact of a particular historical event (e.g., the origin of a novel morphological trait, an episode of biogeographic dispersal, or the onset of an ecological association) on rates of diversification (speciation minus extinction). We describe a Bayesian approach for evaluating the correlation between such events and differential rates of diversification that relies on cross-validation predictive densities. This approach exploits estimates of the marginal posterior probability for the rate of diversification (in the unaffected part of the tree) and the marginal probability for the timing of the event to generate a predictive distribution of species diversity that would be expected had the event not occurred. The realized species diversity can then be compared to this predictive diversity distribution to assess whether rates of diversification associated with the event are significantly higher or lower than expected. Although simple, this Bayesian approach provides a robust inference framework that accommodates various sources of uncertainty, including error associated with estimates of divergence times, diversification-rate parameters, and event history. Furthermore, the proposed approach is relatively flexible, allowing exploration of various types of events (including changes in discrete morphological traits, episodes of biogeographic movement, etc.) under both hypothesis-testing and data-exploration inference scenarios. Importantly, the cross-validation predictive densities approach facilitates evaluation of both replicated and unique historical events. We demonstrate this approach with empirical examples concerning the impact of morphological and biogeographic events on rates of diversification in Adoxaceae and Lupinus, respectively.

可能不错，先放着，慢慢看。

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Genetic compatibility may drive individual mate choice decisions because of predictable fitness effects associated with breeding with incompatible partners. In Gouldian finches (Erythrura gouldiae), females paired with genetically incompatible males of alternative color morphs overproduce sons, presumably to reduce investment in inviable daughters. We also observed a reduced overall investment in clutch size, egg size, and care to offspring resulting from incompatible matings. Within-female experimental pairings demonstrate that female birds have the ability to adaptively adjust the sex of their eggs and allocate resources on the basis of partner quality. Female Gouldian finches thus make cumulative strategic allocation decisions to minimize the costs of poor-quality pairings when faced with a genetically incompatible partner.

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Summary

Three-quarters of leading global food crops rely on animal pollination. With both managed and wild pollinators declining, is there reason for concern? Researchers are beginning to pin down the possible long-term risks.

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Sex allocation in hermaphrodites should evolve in response to changes in the frequency of unisexuals. As predicted, it has now been demonstrated that hermaphrodites respond to the removal of males from experimental plant populations by increasing their allocation to male function.

特别有意义的研究方向。

ABSTRACT

The biogeography of Central America is viewed as a classic case study in understanding the impact of vicariant events on patterns of biotic dispersal. While many biogeographers have focused on community composition and geographical limits of species at broad scales across Central America, much less work has focused on post-colonization diversification patterns at finer scales. The livebearing freshwater fish Xenophallus umbratilis presents an ideal system for determining the impact of recent Earth history events on biodiversity in northern Costa Rica. Here, we test the hypotheses that marine inundation of the San Carlos and northern Limón basins during the Pliocene and Pleistocene has caused genetic fragmentation among X. umbratilis populations, despite contemporary freshwater connections. To test this idea, we collected mitochondrial (cytochrome b) sequence data in 162 individuals taken from 27 localities across northern Costa Rica. We employed a variety of analytical approaches, including: maximum parsimony and maximum likelihood, analysis of molecular variance, and demographic analysis of population size through time. We found four major clades within X. umbratilis, each geographically isolated with no shared haplotypes across drainages. Oddly, clades that occupy adjacent drainages are not always sister taxa in the phylogeny, suggesting that colonization in this species is more complex than a simple model of isolation by distance. All our results are consistent with the hypothesis that changes in sea level associated with glacial eustatic cycles have had an important effect in shaping diversification patterns in this species.

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