Spatially explicit models of divergence and genome hitchhiking

Strong barriers to genetic exchange can exist at divergently selected loci, whereas alleles at neutral loci flow more readily between populations, thus impeding divergence and speciation in the face of gene flow. However, ‘divergence hitchhiking’ theory posits that divergent selection can generate large regions of differentiation around selected loci. ‘Genome hitchhiking’ theory suggests that selection can also cause reductions in average genome‐wide rates of gene flow, resulting in widespread genomic divergence (rather than divergence only around specific selected loci). Spatial heterogeneity is ubiquitous in nature, yet previous models of genetic barriers to gene flow have explored limited combinations of spatial and selective scenarios. Using simulations of secondary contact of populations, we explore barriers to gene flow in various selective and spatial contexts in continuous, two‐dimensional, spatially explicit environments. In general, the effects of hitchhiking are strongest in environments with regular spatial patterning of starkly divergent habitat types. When divergent selection is very strong, the absence of intermediate habitat types increases the effects of hitchhiking. However, when selection is moderate or weak, regular (vs. random) spatial arrangement of habitat types becomes more important than the presence of intermediate habitats per se. We also document counterintuitive processes arising from the stochastic interplay between selection, gene flow and drift. Our results indicate that generalization of results from two‐deme models requires caution and increase understanding of the genomic and geographic basis of population divergence.     

Testing the Performance of Fourteen Native Tropical Tree Species in Two Abandoned Pastures of the Lacandon Rainforest Region of Chiapas,Mexico

The rainforest of Mexico has been degraded and severely fragmented, and urgently require restoration. However, the practice of restoration has been limited by the lack of species‐specific data on survival and growth responses to local environmental variation. This study explores the differential performance of 14 wet tropical early‐, mid‐ or late‐successional tree species that were grown in two abandoned pastures with contrasting land‐use histories. After 18 months, seedling survival and growth of at least 7 of the 14 tree species studied were significantly higher in the site with a much longer history of land use (site 2). Saplings of the three early‐successional species showed exceptional growth rates. However, differences in performance were noted in relation to the differential soil properties between the experimental sites. Mid‐successional species generally showed slow growth rates but high seedling survival, whereas late‐successional species exhibited poor seedling survival at both the study sites. Stepwise linear regressions revealed that the species integrated response index combining survivorship and growth measurements, was influenced mostly by differences in soil pH between the two abandoned pastures. Our results suggest that local environmental variation among abandoned pastures of contrasting land‐use histories influences sapling survival and growth. Furthermore, the similarity of responses among species with the same successional status allowed us to make some preliminary site and species‐specific silvicultural recommendations. Future field experiments should extend the number of species and the range of environmental conditions to identify site “generalists” or more narrowly adapted species, that we would call “sensitive.”     

Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity

The hyper-variable V4 and V9 regions of the small subunit (SSU) rDNA have been targeted for assessing environmental diversity of microbial eukaryotes using next generation sequencing technologies. Here, we explore how the genetic distances among these short fragments compare with the distances obtained from near full-length SSU-rDNA sequences by comparing all pairwise estimates, as well as within and among species of ciliates. Results show that pairwise distances from V4 more closely match the near full-length SSU-rDNA and are more comparable with previous studies based on much longer SSU-rDNA fragments, then pairwise distances from V9. Thus, studies that use the V4 will estimate similar values of phylotype richness and community structure as would have been estimated using the full-length SSU-rDNA.     

Predicting the environmental niche of the genus Phymaturus: Are palluma and patagonicus groups ecologically differentiated?

The genus Phymaturus (Reptilia: Liolaemidae) is distributed in the mountains and rocky plateaux of Argentina and Chile and comprises two groups of species, palluma and patagonicus. The two lineages have diverged early in the evolution of the genus and up to today, there is very little geographical overlap between them. We worked with records of localities from the literature, herpetological collections and field data to evaluate habitat suitability of the genus Phymaturus. We used 11 environmental variables to develop environmental niche models (ENMs) for each group within the genus using the Maxent software, and to determine those variables that best explain the distribution of each group. We also estimated measures of niche similarity using ENMTools to determine whether niche differentiation is real or apparent. The geographical overlap between the groups was very low considering the large geographical range of the genus. Some variables, such as mean annual temperature, soil type and bare soil cover, have a high contribution to the models for both groups. The current niche overlap between Phymaturus groups indicates that the environmental niches of the palluma and patagonicus groups are not equivalent. Based on background analysis, we cannot reject the hypothesis that similarity (or divergence) between groups of Phymaturus is no more than expected based on the availability of habitat. The results of this study are a first approximation to the knowledge of the environmental variables associated with the palluma and patagonicus groups, and reveal that the ecological differences found between these groups are more likely due to habitat availability in their respective regions than to differences in habitat preferences.     

中国畜禽粪便污染现状及产沼气潜力

为弄清中国畜禽粪便排放总量、污染现状及其资源化潜力,通过查阅文献确定了主要估算参数,并结合畜牧业统计数据估算了2009年中国畜禽粪便排放量及其污染物含量、粪便农用地负荷并对畜禽粪便中氮、磷农用地负荷进行预警分级;同时估算了粪便资源沼气潜力。结果表明:2009年中国畜禽养殖业粪便排放总量为32.64亿t鲜重,其中BOD、COD含量分别为7273.95和8039.96万t。全国单位面积农用地畜禽粪便负荷为26.8t·hm-2,氮、磷素负荷分别为158.42和47.92kg·hm-2。预警分级显示:牧区畜禽养殖业对环境不构成威胁;农区除山西、黑龙江外,其他地区均出现不同程度的氮素污染,而磷素的影响在农区普遍存在。2009年畜禽粪便资源沼气潜力约1200亿m3,其中,大中型畜禽养殖场沼气潜力为240亿m3,约合天然气135亿m3。目前沼气工程已成为环境保护和能源结构调整的一种重要手段。     

环境因子对雉鸡甘肃亚种种群遗传多样性的影响(英文)

采用聚合酶链式反应(PCR)和直接测序的方法,测定了雉鸡甘肃亚种9个种群118个样本的线粒体DNA(mtDNA)控制区(D-loop)1150个碱基长度的基因序列,43个变异位点产生51个单倍型。环境因子与种群遗传变异的相关性研究表明,序列变异与经度(r=0.725,P<0.05)、年平均温度(r=0.833,P<0.05)呈显著正相关,核苷酸多样性与经度(r=0.686,P<0.05)、年平均温度(r=0.844,P<0.05)呈显著正相关。片段化与低温是导致雉鸡甘肃亚种遗传多样性的主要因素。序列变异及核苷酸多样性与温度的变异系数呈显著负相关(r序列=-0.679,P<0.05;r核苷酸=-0.669,P<0.05)。温度越稳定地区雉鸡甘肃亚种的遗传多样性越高。     

Histidine kinases in plants: Cross talk between hormone and stress responses

Two-component signaling pathways involve sensory histidine kinases (HK), histidine phosphotransfer proteins (HpT) and response regulators (RR). Recent advancements in genome sequencing projects for a number of plant species have established the TCS family to be multigenic one. In plants, HKs operate through the His–Asp phosphorelay and control many physiological and developmental processes throughout the lifecycle of plants. Despite the huge diversity reported for the structural features of the HKs, their functional redundancy has also been reported via mutant approach. Several sensory HKs having a CHASE domain, transmembrane domain(s), transmitter domain and receiver domain have been reported to be involved in cytokinin and ethylene signaling. On the other hand, there are also increasing evidences for some of the sensory HKs to be performing their role as osmosensor, clearly indicating toward a possible cross-talk between hormone and stress responsive cascades. In this review, we bring out the latest knowledge about the structure and functions of histidine kinases in cytokinin and ethylene signaling and their role(s) in development and the regulation of environmental stress responses.     

A linear ablating system in the left and right atrium: feasibility, catheter performance and clinical results

IntroductionWe describe the use of a ablating system to compartmentalise and regionally isolate the atria in paroxysmal and persistent atrial fibrillation (AF).Methods40 patients were studied, 25 paroxysmal AF and 14 persistent AF. One patient enrolled was later found to be in left atrial flutter and was excluded. The Cardima Revelation® TX catheter system with Intellitemp® Radiofrequency (RF) energy control device and a Medtronic Atakar® RF generator were used to place wide area circumferential ablations to achieve conduction block into the left and right sided pulmonary veins. Roof lines and mitral isthmus lines were also performed. In patients with persistent AF and in repeat procedures, right atrial compartmentalisation was performed with an anterior superior vena cava (SVC) to inferior vena cava (IVC) line and a septal SVC to IVC line.ResultsAt 6 months, 18 of the 39 patients were asymptomatic, 10 had improved symptoms and 22 were in sinus rhythm. In the paroxysmal group, 11 were asymptomatic, 7 had improved symptoms and 16 (64%) were in sinus rhythm. In the persistent group, 7 were asymptomatic, 3 had improved symptoms and 6 (43%) were in sinus rhythm. The total group AF burden was 37.8 ± 5.4 hrs pre-procedure and 23.1 ± 5.1 hrs at 6 months post procedure. Mean temperature, impedance and power recorded at each pole demonstrated effective power delivery at all poles. No catheter charring was observed, complication rates were comparable to standard AF ablation technique.ConclusionLinear ablation in the left and right atria to mimic Cox’s Maze is feasible and safe using this ablating system.