Using density surface models to estimate spatio-temporal changes in population densities and trend

Precise measures of population abundance and trend are needed for species conservation; these are most difficult to obtain for rare and rapidly changing populations. We compare uncertainty in densities estimated from spatio–temporal models with that from standard design-based methods. Spatio–temporal models allow us to target priority areas where, and at times when, a population may most benefit. Generalised additive models were fitted to a 31-year time series of point-transect surveys of an endangered Hawaiian forest bird, the Hawai‘i ‘ākepa Loxops coccineus. This allowed us to estimate bird densities over space and time. We used two methods to quantify uncertainty in density estimates from the spatio–temporal model: the delta method (which assumes independence between detection and distribution parameters) and a variance propagation method. With the delta method we observed a 52% decrease in the width of the design-based 95% confidence interval (CI), while we observed a 37% decrease in CI width when propagating the variance. We mapped bird densities as they changed across space and time, allowing managers to evaluate management actions. Integrating detection function modelling with spatio–temporal modelling exploits survey data more efficiently by producing finer-grained abundance estimates than are possible with design-based methods as well as producing more precise abundance estimates. Model-based approaches require switching from making assumptions about the survey design to assumptions about bird distribution. Such a switch warrants consideration. In this case the model-based approach benefits conservation planning through improved management efficiency and reduced costs by taking into account both spatial shifts and temporal changes in population abundance and distribution.     

Genetic variation in an ephemeral mudflat species: The role of the soil seed bank and dispersal in river and secondary anthropogenic habitats

Many ephemeral mudflat species, which rely on a soil seed bank to build up the next generation, are endangered in their natural habitat due to the widespread regulation of rivers. The aim of the present study was to elucidate the role of the soil seed bank and dispersal for the maintenance of genetic diversity in populations of near‐natural river habitats and anthropogenic habitats created by traditional fish farming practices using Cyperus fuscus as a model. Using microsatellite markers, we found no difference in genetic diversity levels between soil seed bank and above‐ground population and only moderate differentiation between the two fractions. One possible interpretation is the difference in short‐term selection during germination under specific conditions (glasshouse versus field) resulting in an ecological filtering of genotypes out of the reservoir in the soil. River populations harbored significantly more genetic diversity than populations from the anthropogenic pond types. We suggest that altered levels and patterns of dispersal together with stronger selection pressures and historical bottlenecks in anthropogenic habitats are responsible for the observed reduction in genetic diversity. Dispersal is also supposed to largely prohibit genetic structure across Europe, although there is a gradient in private allelic richness from southern Europe (high values) to northern, especially north‐western, Europe (low values), which probably relates to postglacial expansion out of southern and/or eastern refugia.     

Movement of sturgeons (Acipenser oxyrinchus oxyrinchus and A. fulvescens) in the St. Lawrence Estuary: A 35-year tagging study

Movement of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) and lake sturgeon (A. fulvescens) in the St. Lawrence Estuary (Québec, Canada) are not fully understood. To assess the movement extent of both species, a mark–recapture study was conducted in collaboration with commercial fishermen operating in the St. Lawrence Estuary. Between 1981 and 2015, 3,367 Atlantic sturgeon (fork length 21.8–199.5 cm) and 3,180 lake sturgeon (fork length 17.8–190.8 cm) were tagged and released. Of these, 673 Atlantic sturgeon and 42 lake sturgeon were recaptured. The maximum distances traveled between capture and recapture locations were 1,307 km for Atlantic sturgeon (8 years after initial capture) and 252 km for lake sturgeon (less than 1 year after initial capture). Statistical analyses identified differences in the dispersal distance of both species as revealed by a first component characterized by individuals with short dispersal distances (98% and <35 km for Atlantic sturgeon; 58% and <1 km for lake sturgeon) and a second component characterized by individuals with longer dispersal distances (2% and >600 km for Atlantic sturgeon; 42% and >190 km for lake sturgeon). We suggest that the short dispersal distances detected in the vast majority of Atlantic sturgeon recaptures likely reflect strong site fidelity, highlighting the importance of the St. Lawrence Estuary as a preferred habitat for juveniles and subadults. Although recaptures were low for lake sturgeon because this species is only marginally targeted by commercial fishermen in the St. Lawrence Estuary, our results also showed that this species uses estuarine habitats and that half of the population seems to exhibit strong site fidelity (67% of individuals were recaptured within 2 km).     

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.     

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。     

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.