Natural variation in Arabidopsis lyrata vernalization requirement conferred by a FRIGIDA indel polymorphism

Species share homologous genes to a large extent, but it isnot yet known to what degree the same loci have been targetsfor natural selection in different species. Natural variationin flowering time is determined to a large degree by 2 genes,FLOWERING LOCUS C and FRIGIDA, in Arabidopsis thaliana. Here,we examine whether FRIGIDA has a role in differences in floweringtime between and within natural populations of Arabidopsis lyrata,a close outcrossing perennial relative of A. thaliana. We found2 FRIGIDA sequence variants producing potentially functionalproteins but with a length difference of 14 amino acids. Thesevariants conferred a 15-day difference in flowering time inan association experiment in 2 Scandinavian populations. Thedifference in flowering time between alleles was confirmed withtransformation to A. thaliana. Because the north European late-floweringpopulations harbor both late- and early sequence variants atintermediate frequencies and the late-flowering variant is mostfrequent in the southern early flowering European population,other genetic factors must be responsible for the floweringtime differences between the populations. The length polymorphismoccurs at high frequencies also in several North American populations.The occurrence of functional variants at intermediate frequenciesin several populations suggests that the variation may be maintainedby balancing selection. This is in contrast to A. thaliana,where independent loss-of-function mutations at the FRIGIDAgene are responsible for differences between populations andlocal adaptation.     

Geological dates and molecular rates: fish DNA sheds light on time dependency

Knowledge of DNA evolution is central to our understanding of biological history, but how fast does DNA change? Previously, pedigree and ancient DNA studies--focusing on evolution in the short term--have yielded molecular rate estimates substantially faster than those based on deeper phylogenies. It has recently been suggested that short-term, elevated molecular rates decay exponentially over 1-2 Myr to long-term, phylogenetic rates, termed "time dependency of molecular rates." This transition has potential to confound molecular inferences of demographic parameters and dating of many important evolutionary events. Here, we employ a novel approach--geologically dated changes in river drainages and isolation of fish populations--to document rates of mitochondrial DNA change over a range of temporal scales. This method utilizes precise spatiotemporal disruptions of linear freshwater systems and hence avoids many of the limitations associated with typical DNA calibration methods involving fossil data or island formation. Studies of freshwater-limited fishes across the South Island of New Zealand have revealed that genetic relationships reflect past, rather than present, drainage connections. Here, we use this link between drainage geology and genetics to calibrate rates of molecular evolution across nine events ranging in age from 0.007 Myr (Holocene) to 5.0 Myr (Pliocene). Molecular rates of change in galaxiid fishes from calibration points younger than 200 kyr were faster than those based on older calibration points. This study provides conclusive evidence of time dependency in molecular rates as it is based on a robust calibration system that was applied to closely related taxa, and analyzed using a consistent and rigorous methodology. The time dependency observed here appears short-lived relative to previous suggestions (1-2 Myr), which has bearing on the accuracy of molecular inferences drawn from processes operating within the Quaternary and mechanisms invoked to explain the decay of rates with time.     

半圈养条件下东北虎繁殖期的行为时间分配

1998年 10月～ 2 0 0 0年 10月在黑龙江东北虎林园 ,采用随机取样法和瞬时扫描取样法对繁殖期东北虎的行为进行了研究。结果表明 ,在繁殖期的不同阶段东北虎的行为发生较大的变化。在发情交配期雌雄虎的时间分配相似 (P >0 0 5 ) ,均将最多的时间用于运动 ,用于休息的时间较少 ,用于发情交配和其它行为的时间较多。雌虎在妊娠期较多的时间用于休息和运动 ,取食、站立、社会和其它行为的时间均较少 ;产仔期最多的时间用于休息 ,其次是运动 ,用于产仔和其它行为的时间较多 ,用于取食的时间最少 ;哺乳期最多的时间用于休息 ,其次是哺乳和运动 ,用于取食和其它行为的时间较少。活动规律方面 ,各种行为在强度、出现和持续的时间上存在较大差异。单因素方差分析表明 ,在繁殖期的不同阶段雌性东北虎的休息和运动存在极显著差异 (P <0 0 0 1) ,取食存在显著差异 (P <0 0 5 ) ,只有其它行为不存在显著差异(P >0 0 5 )。 10 0日龄内幼虎用于休息的时间最多 ,其次是运动和取食 ,其它行为的时间最少。     

The effect of intra- and interspecific aggression on patch residence time in Negev Desert gerbils: a competing risk analysis

We observed patch-use behavior by two gerbil species in a fieldsetting and investigated how aggression and intrinsic decision-makinginteract to influence patch residence times. Results were interpretedby using a competing risk analysis model, which uniquely enabledus to estimate the intrinsic patch-leaving decisions independentlyof external interruptions of foraging bouts by aggression. Theexperiment was conducted in two 1-ha field enclosures completelysurrounded by rodent-proof fences and included allopatric (onlyGerbillus andersoni allenbyi) and sympatric (G. a. allenbyiand G. pyramidum) treatments. We predicted that increased foodpatch quality (i.e., habitat quality) should decrease intrinsicpatch-leaving rates and increase rates of aggressive interactionsinvolving the forager feeding in the patch (i.e., the occupantindividual). We also anticipated that increasing populationdensity should result in an increase in the rate of aggressiveinteractions involving the occupant individual. Our resultssupported the first two predictions, indicating a trade-offbetween foraging and aggression. However, the third predictionwas realized only for G. a. allenbyi in allopatry. Furthermore,in allopatry, occupant G. a. allenbyi individuals with highcompetitive ranks were involved in aggressive interactions atlower rates than those with low competitive ranks. However,in sympatry, patch-use behavior of occupant G. a. allenbyi individualswas mainly influenced by aggressive behavior of G. pyramidum,which did not respond to their competitive rank. Thus, it shouldpay less for G. a. allenbyi to be aggressive in sympatric populations.The observed reduction in intraspecific aggression among individualG. a. allenbyi in the presence of G. pyramidum supports thisassertion. We suggest that this reduction likely weakens thenegative effect of intra- and interspecific density on the percapita growth rate of G. a. allenbyi. Because this would changethe slope of the isocline of G. a. allenbyi, it could be animportant mechanism promoting coexistence when habitat selectionis constrained.     

从酵母表达时间序列估计基因调控网络

基因调控网络是生命功能在基因表达层面上的展现。用组合线性调控模型、调控元件识别和基因聚类等方法 ,从基因组表达谱解读酵母在细胞周期与环境胁迫中的基因调控网络。结果表明 ,细胞在不同环境条件下会调整基因调控网络。在适应的环境下 ,起主要作用的是细胞生长和增殖有关的基因调控网络 ;而在响应环境胁迫时 ,细胞会再规划调控网络 ,抑制细胞生长和增殖相关的基因 ,诱导跟适应性糖类代谢与结构修复相关的基因 ,还可能启动减数分裂产生孢子。分别从细胞周期和环境胁迫响应相关基因中 ,搜索到转录因子Mcm1结合位点TT CC T GGAAA ,和Dal82在尿囊素代谢途径相关基因上的结合位点TGAAAAWTTT。从而 ,从酵母表达时间序列估计基因调控网络是可行的 ,与至今已知的实验观察相当吻合     

Sequence‐dependent folding and unfolding of ligand‐bound purine riboswitches

Riboswitch regulation of gene expression requires ligand‐mediated RNA folding. From the fluorescence lifetime distribution of bound 2‐aminopurine ligand, we resolve three RNA conformers (C_o, C_i, C_c) of the liganded G‐ and A‐sensing riboswitches from Bacillus subtilis. The ligand binding affinities, and sensitivity to Mg²⁺, together with results from mutagenesis, suggest that C_o and C_i are partially unfolded species compromised in key loop‐loop interactions present in the fully folded C_c. These data verify that the ligand‐bound riboswitches may dynamically fold and unfold in solution, and reveal differences in the distribution of folded states between two structurally homologous purine riboswitches: Ligand‐mediated folding of the G‐sensing riboswitch is more effective, less dependent on Mg²⁺, and less debilitated by mutation, than the A‐sensing riboswitch, which remains more unfolded in its liganded state. We propose that these sequence‐dependent RNA dynamics, which adjust the balance of ligand‐mediated folding and unfolding, enable different degrees of kinetic discrimination in ligand binding, and fine‐tuning of gene regulatory mechanisms. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 953–965, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Odor-mediated patch choice in the parasitoid Venturia canescens: temporal decision dynamics

Parasitoids foraging for hosts in a heterogeneous environment would greatly benefit if they could decide already from a distance in which areas search for resources would be most profitable and to avoid areas of low fitness returns. Interestingly, the temporal dynamics of the decision process in parasitoid patch choice have rarely been investigated. In a Y-tube olfactometer, we tested whether thelytokous and arrhenotokous females of the parasitoid wasp Venturia canescens (Gravenhorst) (Hymenoptera: Ichneumonidae) respond to differences in cues indicating the quality of a host-containing patch and choose more profitable patches. Special attention was given to the time it took females to make their choices (patch choice time) when differences in patch quality were either qualitative (absence vs. presence of hosts and kairomone) or quantitative (various concentrations of hosts and kairomone, and presence of competitors). We found that both thelytokous and arrhenotokous wasps only chose the higher-quality patch based on odor cues when the difference was qualitative. When patches differed only with respect to the number of hosts, or the presence or absence of competing female parasitoids, no significant preference could be found in females of either strain of the parasitoid. In contrast, both the time until females reached the junction of the Y-tube olfactometer (response time) and the time until females decided for either patch (decision time) varied with parasitoid strain and odor treatment. Thelytokous wasps were faster than arrhenotokous wasps in their response time and in their decision time. However, females of both strains responded faster with increasing number of total hosts releasing kairomone. Yet, decision time for patches did not significantly vary as a function of patch quality offered to Venturia wasps.