Biogeography and evolution of a widespread Central American lizard species complex: Norops humilis, (Squamata: Dactyloidae)

Background

Caribbean anole lizards (Dactyloidae) have frequently been used as models to study questions regarding biogeography and adaptive radiations, but the evolutionary history of Central American anoles (particularly those of the genus Norops) has not been well studied. Previous work has hypothesized a north-to-south dispersal pattern of Central American Norops, but no studies have examined dispersal within any Norops lineages. Here we test two major hypotheses for the dispersal of the N. humilis/quaggulus complex (defined herein, forming a subset within Savage and Guyer’s N. humilis group).

Results

Specimens of the N. humilis group were collected in Central America, from eastern Mexico to the Canal Zone of Panama. Major nodes were dated for comparison to the geologic history of Central America, and ancestral ranges were estimated for the N. humilis/quaggulus complex to test hypothesized dispersal patterns. These lineages displayed a northward dispersal pattern. We also demonstrate that the N. humilis/quaggulus complex consists of a series of highly differentiated mitochondrial lineages, with more conserved nuclear evolution. The paraphyly of the N. humilis species group is confirmed. A spatial analysis of molecular variance suggests that current populations are genetically distinct from one another, with limited mitochondrial gene flow occurring among sites.

Conclusions

The observed south-to-north colonization route within the Norops humilis/quaggulus complex represents the first evidence of a Norops lineage colonizing in a south-to-north pattern, (opposite to the previously held hypothesis for mainland Norops). One previously described taxon (N. quaggulus) was nested within N. humilis, demonstrating the paraphyly of this species; while our analyses also reject the monophyly of the Norops humilis species group (sensu Savage and Guyer), with N. tropidonotus, N. uniformis, and N. marsupialis being distantly related to/highly divergent from the N. humilis/quaggulus complex. Our work sheds light on mainland anole biogeography and past dispersal events, providing a pattern to test against other groups of mainland anoles.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0391-4) contains supplementary material, which is available to authorized users.     

Distinctive expansion of gene families associated with plant cell wall degradation,secondary metabolism,and nutrient uptake in the genomes of grapevine trunk pathogens

Background

Trunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development.

Results

The integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution.

Conclusions

This study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1624-z) contains supplementary material, which is available to authorized users.     

SV-AUTOPILOT: optimized,automated construction of structural variation discovery and benchmarking pipelines

Background

Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for other species. Objectives of this work included:

1. Creating an automated, standardized pipeline for SV prediction.
2. Identifying the best tool(s) for SV prediction through benchmarking.
3. Providing a statistically sound method for merging SV calls.

Results

The SV-AUTOPILOT meta-tool platform is an automated pipeline for standardization of SV prediction and SV tool development in paired-end next-generation sequencing (NGS) analysis. SV-AUTOPILOT comes in the form of a virtual machine, which includes all datasets, tools and algorithms presented here. The virtual machine easily allows one to add, replace and update genomes, SV callers and post-processing routines and therefore provides an easy, out-of-the-box environment for complex SV discovery tasks. SV-AUTOPILOT was used to make a direct comparison between 7 popular SV tools on the Arabidopsis thaliana genome using the Landsberg (Ler) ecotype as a standardized dataset. Recall and precision measurements suggest that Pindel and Clever were the most adaptable to this dataset across all size ranges while Delly performed well for SVs larger than 250 nucleotides. A novel, statistically-sound merging process, which can control the false discovery rate, reduced the false positive rate on the Arabidopsis benchmark dataset used here by >60%.

Conclusion

SV-AUTOPILOT provides a meta-tool platform for future SV tool development and the benchmarking of tools on other genomes using a standardized pipeline. It optimizes detection of SVs in non-human genomes using statistically robust merging. The benchmarking in this study has demonstrated the power of 7 different SV tools for analyzing different size classes and types of structural variants. The optional merge feature enriches the call set and reduces false positives providing added benefit to researchers planning to validate SVs. SV-AUTOPILOT is a powerful, new meta-tool for biologists as well as SV tool developers.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1376-9) contains supplementary material, which is available to authorized users.     

Enhanced Genetic Analysis of Single Human Bioparticles Recovered by Simplified Micromanipulation from Forensic ‘Touch DNA’ Evidence

DNA profiles can be obtained from ‘touch DNA’ evidence, which comprises microscopic traces of human biological material. Current methods for the recovery of trace DNA employ cotton swabs or adhesive tape to sample an area of interest. However, such a ‘blind-swabbing’ approach will co-sample cellular material from the different individuals, even if the individuals’ cells are located in geographically distinct locations on the item. Thus, some of the DNA mixtures encountered in touch DNA samples are artificially created by the swabbing itself. In some instances, a victim’s DNA may be found in significant excess thus masking any potential perpetrator’s DNA.In order to circumvent the challenges with standard recovery and analysis methods, we have developed a lower cost, ‘smart analysis’ method that results in enhanced genetic analysis of touch DNA evidence. We describe an optimized and efficient micromanipulation recovery strategy for the collection of bio-particles present in touch DNA samples, as well as an enhanced amplification strategy involving a one-step 5 µl microvolume lysis/STR amplification to permit the recovery of STR profiles from the bio-particle donor(s). The use of individual or few (i.e., “clumps”) bioparticles results in the ability to obtain single source profiles. These procedures represent alternative enhanced techniques for the isolation and analysis of single bioparticles from forensic touch DNA evidence. While not necessary in every forensic investigation, the method could be highly beneficial for the recovery of a single source perpetrator DNA profile in cases involving physical assault (e.g., strangulation) that may not be possible using standard analysis techniques. Additionally, the strategies developed here offer an opportunity to obtain genetic information at the single cell level from a variety of other non-forensic trace biological material.     

Antioxidant Capacity and Chemical Profiles of Satureja montana L. Honey: Hotrienol and Syringyl Derivatives as Biomarkers

The present study is focused on the antioxidant capacity and chemical profiling of eight Croatian Satureja montana L. honey samples. Among the 20 compounds obtained by headspace solid‐phase microextraction (HS‐SPME) and identified by GC‐FID and GC/MS analyses, hotrienol was predominant (75.9–81.7%). The honey matrix volatile/semivolatile profile was investigated by ultrasonic solvent extraction (USE) followed by GC‐FID and GC/MS analyses. The major compounds identified by this latter method were the sinapic‐acid derivatives methyl syringate (36.2–72.8%) and syringaldehyde (2.2–43.1%). Direct, targeted HPLC‐DAD analyses of the native honey samples revealed the presence of methyl syringate (7.10–39.60 mg/kg) and syringic acid (0.10–1.70 mg/kg). In addition, the total phenolic content of the samples was determined by the Folin? Ciocalteu assay (311.0–465.9 mg GAE/kg), and the antioxidant capacity was evaluated by the DPPH radical‐scavenging activity (0.5–1.0 mmol TEAC/kg) and the ferric reducing antioxidant power (2.5–5.1 mmol Fe²⁺/kg).     

福建省近年来审(认)定花生品种的遗传多样性分析

以近年来通过福建省审(认)定的23个花生品种为材料,对株型、叶形、叶片大小、叶色、荚果形状、网纹粗细、网纹深浅、开花习性、种仁大小、种皮颜色和粒形共11个表型性状的Simpson遗传多样性指数(简称SI)和Shannon-Weaver遗传多样性指数(简称H')进行了分析。结果表明:除开花习性、种皮颜色和种仁大小3个性状表现一致外,23个品种的遗传多样性指数分别为SI=0.506,H'=0.796,其中以荚果形状最低(SI=0.237,H'=0.387),以网纹粗细最高(SI=0.755,H'=1.335);从50对引物中筛选出9条多态性较好引物,共扩增出59条多态性条带,平均每对引物可扩增6.56条多态性条带,引物的多态性信息含量(PIC)变幅为0.746~0.957,平均值为0.88。23个品种间的遗传相似系数在0.225~0.818,平均为0.579。在相似系数0.55处可分为3个类群。系谱分析表明亲本来源相近的品种优先聚在一起,利用辐照诱变材料对于拓宽花生遗传基础发挥作用较明显。SSR分析结果基本上与系谱分析的结果相吻合。     

医院急诊创伤评分的临床应用价值分析

目的:研究分析医院急诊创伤评分(ETS)的临床应用价值,为急诊抢救提供更加合适的临床方案。方法:选择2012年6月至2013年6月在我院急诊抢救的90例患者作为研究对象。以数字法随机分成观察组和对照组,每组各45例。对照组由抢救医师依照患者病史、症状及体征进行急救诊断;观察组则由抢救医师根据ETS评分进行记录判定,辅助其作出急救诊断。统计并对比两组患者急救情况、院内转运时间及抢救时间,分析影响患者抢救成功的危险因素。结果:观察组患者在明确诊断及抢救成功方面的比例均显著高于对照组,但死亡率显著低于对照组,差异均有统计学意义(均P0.05)。观察组的院内转运时间及抢救时间均显著少于对照组,差异均有统计学意义(均P0.05)。Logistic回归分析显示,年龄60岁,未使用ETS评分及合并多处创伤均为影响患者抢救成功的危险因素。结论:ETS评分可较好的判定出急诊创伤患者的伤情,利于抢救治疗,有效增加抢救成功率,值得临床推荐。     

Tree height–diameter allometry across the United States

The relationship between tree height and diameter is fundamental in determining community and ecosystem structure as well as estimates of biomass and carbon storage. Yet our understanding of how tree allometry relates to climate and whole organismal function is limited. We used the Forest Inventory and Analysis National Program database to determine height–diameter allometries of 2,976,937 individuals of 293 tree species across the United States. The shape of the allometric relationship was determined by comparing linear and nonlinear functional forms. Mixed‐effects models were used to test for allometric differences due to climate and floristic (between angiosperms and gymnosperms) and functional groups (leaf habit and shade tolerance). Tree allometry significantly differed across the United States largely because of climate. Temperature, and to some extent precipitation, in part explained tree allometric variation. The magnitude of allometric variation due to climate, however, had a phylogenetic signal. Specifically, angiosperm allometry was more sensitive to differences in temperature compared to gymnosperms. Most notably, angiosperm height was more negatively influenced by increasing temperature variability, whereas gymnosperm height was negatively influenced by decreasing precipitation and increasing altitude. There was little evidence to suggest that shade tolerance influenced tree allometry except for very shade‐intolerant trees which were taller for any given diameter. Tree allometry is plastic rather than fixed and scaling parameters vary around predicted central tendencies. This allometric variation provides insight into life‐history strategies, phylogenetic history, and environmental limitations at biogeographical scales.     

双歧杆菌制剂辅助治疗儿童抗生素相关性腹泻的系统评价与Meta分析

目的评价双歧杆菌制剂辅助治疗儿童抗生素相关性腹泻的临床疗效。方法检索CNKI、维普、万方、PubMed、Embase等数据库,时间为建库至2019年8月,筛选随机对照试验(randomized controlled tests,RCTs)。采用RevMan 5.3软件对纳入的研究进行Meta分析,采用Cochrane系统评价工具评估文献发表偏倚。结果共纳入7篇较高质量的RCTs,Meta分析结果示:RR=1.21,95%CI=(1.14,1.27),Z=6.80,P0.01。结论双歧杆菌制剂可有效提高患者的总有效率,改善患者症状。但纳入文献存在一定的发表偏倚,仍需要更多的研究数据加以验证。