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Gene conversion has a central role in the evolutionary fine-tuning of regulatory elements in the fruit fly Drosophila miranda.</jats:p

The Pattern of Polymorphism on Human Chromosome 21

Polymorphism data from 20 partially resequenced copies of human chromosome 21—more than 20,000 polymorphic sites—were analyzed. The allele-frequency distribution shows no deviation from the simplest population genetic model with a constant population size (although we show that our analysis has no power to detect population growth). The average rate of recombination per site is estimated to be roughly one-half of the rate of mutation per site, again in agreement with simple model predictions. However, sliding-window analyses of the amount of polymorphism and the extent of linkage disequilibrium (LD) show significant deviations from standard models. This could be due to the history of selection or demographic change, but it is impossible to draw strong conclusions without much better knowledge of variation in the relationship between genetic and physical distance along the chromosome

A statistical test for the difference in the amounts of DNA variation between two populations

A statistical test for the difference in the amounts of DNA variation between two populations is developed. The test statistic involves the covariance of the amount of variation between two populations, which is given by a function of their divergence time, T0. Accordingly, the power (rejection probability) of the test depends on T0. In this article, T0 is treated as unknown because it is very difficult to estimate. The test is most conservative when T0 = ∞ is assumed because the covariance is zero. If T0 = 0 is assumed, the largest value of the rejection probability is obtained. Thus, the test provides a range of rejection probability unless we have a reliable estimate of T0. The test is applied to the PgiC region in three mustard species: Leavenworthia stylosa, L. crassa and L. uniflora. The results of our test show that the level of variation in L. stylosa is significantly higher than those in the other species

Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions

Prokaryotic organisms share genetic material across species boundaries by means of a process known as horizontal gene transfer (HGT). This process has great significance for understanding prokaryotic genome diversification and unraveling their complexities. Phylogeny-based detection of HGT is one of the most commonly used methods for this task, and is based on the fundamental fact that HGT may cause gene trees to disagree with one another, as well as with the species phylogeny. Using these methods, we can compare gene and species trees, and infer a set of HGT events to reconcile the differences among these trees. In this paper, we address three factors that confound the detection of the true HGT events, including the donors and recipients of horizontally transferred genes. First, we study experimentally the effects of error in the estimated gene trees (statistical error) on the accuracy of inferred HGT events. Our results indicate that statistical error leads to overestimation of the number of HGT events, and that HGT detection methods should be designed with unresolved gene trees in mind. Second, we demonstrate, both theoretically and empirically, that based on topological comparison alone, the number of HGT scenarios that reconcile a pair of species/gene trees may be exponential. This number may be reduced when branch lengths in both trees are estimated correctly. This set of results implies that in the absence of additional biological information, and/or a biological model of how HGT occurs, multiple HGT scenarios must be sought, and efficient strategies for how to enumerate such solutions must be developed. Third, we address the issue of lineage sorting, how it confounds HGT detection, and how to incorporate it with HGT into a single stochastic framework that distinguishes between the two events by extending population genetics theories. This result is very important, particularly when analyzing closely related organisms, where coalescent effects may not be ignored when reconciling gene trees. In addition to these three confounding factors, we consider the problem of enumerating all valid coalescent scenarios that constitute plausible species/gene tree reconciliations, and develop a polynomial-time dynamic programming algorithm for solving it. This result bears great significance on reducing the search space for heuristics that seek reconciliation scenarios. Finally, we show, empirically, that the locality of incongruence between a pair of trees has an impact on the numbers of HGT and coalescent reconciliation scenarios

QTL Map Meets Population Genomics: An Application to Rice

Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance

The Power of QTL Mapping with RILs

QTL (quantitative trait loci) mapping is commonly used to identify genetic regions responsible to important phenotype variation. A common strategy of QTL mapping is to use recombinant inbred lines (RILs), which are usually established by several generations of inbreeding of an F1 population (usually up to F6 or F7 populations). As this inbreeding process involves a large amount of labor, we are particularly interested in the effect of the number of inbreeding generations on the power of QTL mapping; a part of the labor could be saved if a smaller number of inbreeding provides sufficient power. By using simulations, we investigated the performance of QTL mapping with recombinant inbred lines (RILs). As expected, we found that the power of F4 population could be almost comparable to that of F6 and F7 populations. A potential problem in using F4 population is that a large proportion of RILs are heterozygotes. We here introduced a new method to partly relax this problem. The performance of this method was verified by simulations with a wide range of parameters including the size of the segregation population, recombination rate, genome size and the density of markers. We found our method works better than the commonly used standard method especially when there are a number of heterozygous markers. Our results imply that in most cases, QTL mapping does not necessarily require RILs at F6 or F7 generations; rather, F4 (or even F3) populations would be almost as useful as F6 or F7 populations. Because the cost to establish a number of RILs for many generations is enormous, this finding will cause a reduction in the cost of QTL mapping, thereby accelerating gene mapping in many species

The rate and tract length of gene conversion between duplicated genes

Interlocus gene conversion occurs such that a certain length of DNA fragment is non-reciprocally transferred (copied and pasted) between paralogous regions. To understand the rate and tract length of gene conversion, there are two major approaches. One is based on mutation-accumulation experiments, and the other uses natural DNA sequence variation. In this review, we overview the two major approaches and discuss their advantages and disadvantages. In addition, to demonstrate the importance of statistical analysis of empirical and evolutionary data for estimating tract length, we apply a maximum likelihood method to several data sets

The way to organizational longevity - Balancing stability and change in Shinise firms

THE WAY TO ORGANIZATIONAL LONGEVITY – Balancing stability and change in Shinise firms The overall purpose of this dissertation is to investigate the secret of longevity in Shinise firms. On the basic assumption that organizational longevity is about balancing stability and change, the theoretical perspectives incorporate routine practice, organizational culture, and organizational identity. These theories explain stability and change in an organization separately and in combination. Qualitative inductive theory building was used in the study. Overall, the empirical data comprised 75 in-depth and semi-structured interviews, 137 archival materials, and observations made over 17 weeks. According to the empirical findings, longevity in Shinise firms is attributable to the internal mechanisms (Shinise tenacity, stability in motion, and emergent change) to secure a balance between stability and change, the continuing stability of the socio-cultural environment in the local community, and active interaction between organizational and local cultures. The contribution of the study to the literature on organizational longevity and the alternative theoretical approaches is first, in theorizing the mechanisms of Shinise tenacity and cross-level cultural dynamism, and second, in pointing out the critical role of: the way firms set their ultimate goal, the dynamism in culture, and the effect of history of the firm to the current business in securing longevity. KEY WORDS Change; Culture; Organizational identity; Organizational longevity; Routines; Shinise firms; Stability; Qualitative researchTIE ORGANISAATION PITKÄIKÄISYYTEEN – vakauden ja muutoksen tasapainottelu shinise-yrityksissä Tämän väitöskirjan tarkoituksena on tutkia shinise-yritysten pitkäikäisyyden salaisuutta. Väitöskirjan lähtökohtana on, että organisatorinen pitkäikäisyys perustuu vakauden ja muutoksen tasapainotteluun. Näin ollen väitöskirja pohjaa rutiinit käytäntöinä-, organisaatiokulttuurin ja organisaatioidentiteetin teorioihin, jotka selittävät niin yhdessä kuin erikseen vakautta ja muutosta organisaatioissa. Menetelmällisesti tutkimuksen lähtökohtana on laadullinen induktiivinen teorian rakentaminen. Empiirinen aineisto koostuu 75 puolistrukturoidusta tai syvähaas- tattelusta, 137 arkistodokumentista, sekä havainnoinnista 17 viikon ajanjaksolta. Empiiristen tulosten perusteella shinise-yritysten pitkäikäisyys pohjautuu kol- meen eri elementtiin: (1) yritysten sisäisiin mekanismeihin (shinise-sinnikkyys, vakaus liikkeessä ja muotoutuva muutos) vakauden ja muutoksen tasapainon turvaamiseksi; (2) paikallisen yhteisön sosio-kulttuurisen ympäristön jatkuvaan vakauteen; sekä (3) yrityskulttuurin ja paikallisen kulttuurin aktiiviseen vuoro- vaikutukseen. Väitöskirja kontribuoi organisaation pitkäikäisyyttä käsittelevään kirjallisuuteen sekä vaihtoehtoisiin teoreettisiin lähestymistapoihin kahdella tavalla: Yhtäältä, se teorisoi shinise-sinnikkyyden sekä kulttuuritasot ylittävän dynamiikan mekanismeja. Toisaalta, se osoittaa miten kriittinen rooli liiketoimin- nan pitkäikäisyyteen on (1) yritysten tavoitteiden asettamistavalla, (2) kulttuurin dynamiikalla ja (3) yrityksen historian vaikutuksella sen nykyiseen liiketoimin- taan. AVAINSANAT Muutos; Organisaatioidentiteetti; Organisaation pitkäikäisyys; Rutiinit; Shinise- yritykset; Vakaus; Laadullinen tutkimussiirretty Doriast

Secret for the longevity in Japanese Shinise companies : values and artifacts

Siirretty Doriast