The use and misuse of regression models in landscape genetic analyses

The field of landscape genetics has been rapidly evolving, adopting and adapting analytical frameworks to address research questions. Current studies are increasingly using regression‐based frameworks to infer the individual contributions of landscape and habitat variables on genetic differentiation. This paper outlines appropriate and inappropriate uses of multiple regression for these purposes, and demonstrates through simulation the limitations of different analytical frameworks for making correct inference. Of particular concern are recent studies seeking to explain genetic differences by fitting regression models with effective distance variables calculated independently on separate landscape resistance surfaces. When moving across the landscape, organisms cannot respond independently and uniquely to habitat and landscape features. Analyses seeking to understand how landscape features affect gene flow should model a single conductance or resistance surface as a parameterized function of relevant spatial covariates, and estimate the values of these parameters by linking a single set of resistance distances to observed genetic dissimilarity via a loss function. While this loss function may involve a regression‐like step, the associated nuisance parameters are not interpretable in terms of organismal movement and should not be conflated with what is actually of interest: the mapping between spatial covariates and conductance/resistance. The growth and evolution of landscape genetics as a field has been rapid and exciting. It is the goal of this paper to highlight past missteps and demonstrate limitations of current approaches to ensure that future use of regression models will appropriately consider the process being modeled, which will provide clarity to model interpretation.     

The Bio3D packages for structural bioinformatics

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ .     

Improved durable pulmonary vein isolation with shorter procedure times and lower energy levels using RF ablation with ablation index and a stringent lesion contiguity

BackgroundThe single procedure success rates of durable pulmonary vein isolation (PVI) for paroxysmal atrial fibrillation (PAF) varies between 80 and 90%. Ablation index, incorporating contact force, stability, time and power is a more profound parameter of significant lesion size and has been established. Equally important is a stringent contiguity of the lesion set.Methods and resultsA total number of 100 consecutive patients undergoing de-novo catheter ablation for paroxysmal atrial fibrillation (PAF) were analyzed between 2016 and 2019. In the first 50 patients (group A) PVI was performed using a surround flow, contact force catheter (Biosense Webster Thermocool STSF, Biosense Webster, USA) with a drag-and-ablate technique to encircle the PVs. In the following 50 patients (group B), PVI was performed using ablation index and a stringent lesion contiguity with an interlesion distance (ILD) of <5 mm. The baseline characteristics showed no significant differences between both groups. During a mean follow-up of 18 ± 3 months after a single procedure, 36 (72%) patients of group A were free of arrhythmia recurrence versus 43 (86%) patients in group B (p = 0.047). A total of 14 patients (group A: 10 (20%), group B: 4 (8%); underwent a redo-procedure. 7 patients of group A (14%) and 2 patients of group B (4%) showed recovered veins. In 3 patients of group A and 2 patients of group B the PVs were durably isolated. In these patients persistent AF recurrence was caused by extra-PV AF sources. Four patients of group A and three patients of group B had continued paroxysmal or persistent AF but did not undergo redo-procedure. With regard to the procedural data, the procedure time, the total energy and the fluoroscopy time were significantly lower in group B (AI and ILD <5 mm) (128.86 ± 18.19 versus 115.35 ± 15.38; p < 0.05; 1619.16 ± 988.56 versus 1186.26 ± 756.34; p < 0.05; 11.49 ± 3.20 versus 9.66 ± 3.86; p = 0.04). Both procedures were performed with a low number of complications, no pericardial effusion was seen in either group.ConclusionsPVI using ablation index in combination with a stringent lesion contiguity improves clinical outcome after first-time PVI with lower PVI recovery, shorter procedure times, lower total energy and shorter fluoroscopy times and therefore, is more efficient.     

起测径对南盘江流域次生林中枯立木空间结构的影响

树木大小是林分的基础属性,反映个体在森林生态系统过程中扮演的角色和地位。作者于2016-2018年在中国西南地区南盘江流域松栎混交林中建立3块永久性标准固定样地(A、B、C),并用双相关函数g(r)、标记相关函数k_(mm)(r)、标记变差函数γ(r)和k-邻体距离分布函数D~k(r)分析不同大小枯立木的空间结构特征,以揭示林分水平上枯立木的大小和空间结构之间的关系。结果显示:(1)枯立木的起测径(minimum measured diameter, mmd)越小,小尺度上(r=0～5 m)的分布格局趋向聚集状态,但随着起测径的增大(mmd=5～8 cm),随机分布格局几乎占据每个尺度(r=0～20 m)。(2)当起测径等于1～2 cm时,枯立木的大小在小尺度上(r=0～1 m)接近聚集分布,除此之外它一直保持随机分布。(3)当起测径≤4 cm时,枯立木的树种分布集中;反之,它在每个尺度上越接近或成为随机状态。(4)当起测径由1 cm增大至8 cm时,r=0～10 m之内相邻木的株数减少且距离增加,其变化程度受到林分株数的影响。研究表明,枯立木的起测径与其分布格局类型、标记特征以及距离分布紧密相关,暗示同种小树易呈团块死亡,而大径的枯立木偏向随机分布;对比分析枯死木的空间结构需使用统一的起测径标准。     

沙生植物沙鞭不同居群形态变异研究

以沙鞭(Psammochloa villosa Bor.)20个自然居群为研究对象,对其株高、花序长度、旗叶长度、旗叶宽度和小穗长度等12个表型性状进行形态变异研究。结果显示,12个性状群体间F值为1.832~8.958,达到显著或极显著水平,表明沙鞭不同居群表型性状存在广泛变异,且变异程度各不相同;主成分分析结果显示,前4个主成分代表了沙鞭形态多样性的82.277%,其中旗叶长度、旗叶宽度、颖片长度、小穗长度等是造成不同居群表型性状差异的主要因素;依据欧式距离对参试居群进行的UPGMA聚类分析结果表明,当遗传距离为20.5时,可以将20个沙鞭野生居群划分为两类,且各表型性状并没有依居群地理分布而聚类。     

植食性昆虫的嗅觉选食过程及其机制研究进展

植食性昆虫的嗅觉在其选择食物的过程中发挥了重要的作用,它能通过对植物挥发物的感受来定向和定位食物源并产生趋近行为,进而根据特殊的化合物或者多种化合物的特异浓度组合来区分寄主和非寄主植物.在这个过程中,昆虫嗅觉器官上相关的嗅觉感受蛋白被植物挥发物激活,形成特异的嗅觉感受通路,在行为上调控昆虫嗅觉选食的能力.本文主要从植食性昆虫嗅觉选食过程中植物挥发物的散布特征、昆虫识别植物信息的嗅觉感受机制及其相关的分子基础等方面进行叙述,同时讨论了近年的研究成果并展望了下一步的研究方向.     

Examination of host-taxon,environment, and distance effects on leaf fungal endophytes in the dominant woody genus,Metrosideros, on Oʻahu

Fungal endophyte (FE) communities can be shaped by environmental conditions and/or host-plant affinities. Hawaiʻi's landscape-dominant woody genus Metrosideros (Myrtaceae) comprises several vegetatively distinct taxa that are non-randomly distributed across environments, and their FE communities are poorly known. We examined the relative importance of Metrosideros taxon and environment (elevation) on FE communities on Oʻahu. ITS1 rDNA barcoding and sequencing of 113 trees detected a richness of 1,637 FEs representing 5 phyla, 223 genera, and 200 species. Variation in FE diversity was significantly explained by host taxon and site with considerable overlap in FE communities among taxa. FE communities did not vary between pubescent and glabrous taxa or across elevations, possibly due to the relatively narrow range of environmental conditions represented on Oʻahu relative to taller islands. A significant pattern of isolation by distance in FE composition was detected both among and within sites, consistent with restricted dispersal of FEs across the island.     

Parallel speciation or long‐distance dispersal? Lessons from seaweeds (Fucus) in the Baltic Sea

Parallel evolution has been invoked as a forceful mechanism of ecotype and species formation in many animal taxa. However, parallelism may be difficult to separate from recently monophyletically diverged species that are likely to show complex genetic relationships as a result of considerable shared ancestral variation and secondary hybridization in local areas. Thus, species' degrees of reproductive isolation, barriers to dispersal and, in particular, limited capacities for long‐distance dispersal will affect demographical structures underlying mechanisms of divergent evolution. Here, we used nine microsatellite DNA markers to study intra‐ and interspecific genetic diversity of two recently diverged species of brown macroalgae, Fucus radicans (L. Bergström & L. Kautsky) and F. vesiculosus (Linnaeus), in the Baltic Sea. We further performed biophysical modelling to identify likely connectivity patterns influencing the species' genetic structures. For each species, we found intraspecific contrasting patterns of clonality incidence and population structure. In addition, strong genetic differentiation between the two species within each locality supported the existence of two distinct evolutionary lineages (F_ST = 0.15–0.41). However, overall genetic clustering analyses across both species' populations revealed that all populations from one region (Estonia) were more genetically similar to each other than to their own taxon from the other two regions (Sweden and Finland). Our data support a hypothesis of parallel speciation. Alternatively, Estonia may be the ancestral source of both species, but is presently isolated by oceanographic barriers to dispersal. Thus, a limited gene flow in combination with genetic drift could have shaped the seemingly parallel structure.     

Predicting the structural integrity of bone defects repaired using bone graft materials

Bone defects create stress concentrations which can cause fracture under impact or cyclic loading. Defects are often repaired by filling them with a bone graft material; this will reduce the stress concentration, but not completely, because these materials have lower stiffness than bone. The fracture risk decreases over time as the graft material is replaced by living bone. Many new bone graft materials are being developed, using tissue engineering and other techniques, but currently there is no rational way to compare these materials and predict their effectiveness in repairing a given defect. This paper describes, for the first time, a theoretical model which can be used to predict failure by brittle fracture or fatigue, initiating at the defect. Preliminary results are presented, concentrating on the prediction of stress fracture during the crucial post-operative period. It is shown that the likelihood of fracture is strongly influenced by the shape of the defect as well as its size, and also by the level of post-operative exercise. The most important finding is that bone graft materials can be successful in preventing fracture even when their mechanical properties are greatly inferior to those of bone. Future uses of this technique include pre-clinical assessment of bone replacement materials and pre-operative planning in orthopaedic surgery.