Detecting multivariate interactions in spatial point patterns with Gibbs models and variable selection

We propose a method for detecting significant interactions in very large multivariate spatial point patterns. This methodology develops high dimensional data understanding in the point process setting. The method is based on modelling the patterns using a flexible Gibbs point process model to directly characterise point-to-point interactions at different spatial scales. By using the Gibbs framework significant interactions can also be captured at small scales. Subsequently, the Gibbs point process is fitted using a pseudo-likelihood approximation, and we select significant interactions automatically using the group lasso penalty with this likelihood approximation. Thus we estimate the multivariate interactions stably even in this setting. We demonstrate the feasibility of the method with a simulation study and show its power by applying it to a large and complex rainforest plant population data set of 83 species

Directional genetic differentiation and asymmetric migration

Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly used to gather this information. One potential caveat is that these measures assume gene flow to be symmetric. However, asymmetric gene flow is common in nature, especially in systems driven by physical processes such as wind or water currents. Since information about levels of asymmetric gene flow among populations is essential for the correct interpretation of the distribution of contemporary genetic diversity within species, this should not be overlooked. To obtain information on asymmetric migration patterns from genetic data, complex models based on maximum likelihood or Bayesian approaches generally need to be employed, often at great computational cost. Here, a new simpler and more efficient approach for understanding gene flow patterns is presented. This approach allows the estimation of directional components of genetic divergence between pairs of populations at low computational effort, using any of the classical or modern measures of genetic differentiation. These directional measures of genetic differentiation can further be used to calculate directional relative migration and to detect asymmetries in gene flow patterns. This can be done in a user-friendly web application called divMigrate-online introduced in this paper. Using simulated data sets with known gene flow regimes, we demonstrate that the method is capable of resolving complex migration patterns under a range of study designs.Comment: 25 pages, 8 (+3) figures, 1 tabl

Modelling spatial biodiversity in the world’s largest mangrove ecosystem-The Bangladesh Sundarbans: a baseline for conservation

Aim: Mangrove forests are among the most threatened and rapidly vanishing, but poorly understood ecosystems. We aim to uncover the variables driving mangrove biodiversity and produce baseline biodiversity maps for the Sundarbans world heritage site—the Earth's largest contiguous mangrove ecosystem. Location: The Bangladesh Sundarbans, South Asia. Methods: We collected species abundance, environmental and disturbance data from 110 permanent sample plots (PSPs) covering the entire Bangladesh Sundarbans (6,017 km2). We applied generalized additive models to determine the key variables shaping the spatial distributions of mangrove diversity and community composition. Biodiversity maps were constructed using covariate‐driven habitat models, and their predictive performances were compared with covariate‐free (i.e., direct interpolation) approaches to see whether the inclusion of habitat variables bolster spatial predictions of biodiversity or whether we can rely on direct interpolation approaches when environmental data are not available. Results: Historical forest exploitation, disease, siltation and soil alkalinity were the key stressors causing loss of alpha and gamma diversity in mangrove communities. Both alpha and gamma diversity increased along the downstream‐to‐upstream and riverbank‐to‐forest interior gradients. Mangrove communities subjected to intensive past tree harvesting, disease outbreaks and siltation were more homogeneous in species composition (beta diversity). In contrast, heterogeneity in species composition increased along decreasing salinity and downstream‐to‐upstream gradients. We find that the surviving biodiversity hotspots (comprising many globally endangered tree species) are located outside the established protected area network and hence open to human exploitation. We therefore suggest bringing them immediately under protected area management. Main Conclusions: We provide the first habitat‐based modelling and mapping of alpha, beta and gamma diversity in threatened mangrove communities. In general, habitat‐based models showed better predictive ability than the covariate‐free approach. Nevertheless, the small margin of differences between the approaches demonstrates the utility of direct interpolation approaches when environmental data are unavailable

Optimizing passive acoustic sampling of bats in forests

Passive acoustic methods are increasingly used in biodiversity research and monitoring programs because they are cost-effective and permit the collection of large datasets. However, the accuracy of the results depends on the bioacoustic characteristics of the focal taxa and their habitat use. In particular, this applies to bats which exhibit distinct activity patterns in three-dimensionally structured habitats such as forests. We assessed the performance of 21 acoustic sampling schemes with three temporal sampling patterns and seven sampling designs. Acoustic sampling was performed in 32 forest plots, each containing three microhabitats: forest ground, canopy, and forest gap. We compared bat activity, species richness, and sampling effort using species accumulation curves fitted with the clench equation. In addition, we estimated the sampling costs to undertake the best sampling schemes. We recorded a total of 145,433 echolocation call sequences of 16 bat species. Our results indicated that to generate the best outcome, it was necessary to sample all three microhabitats of a given forest location simultaneously throughout the entire night. Sampling only the forest gaps and the forest ground simultaneously was the second best choice and proved to be a viable alternative when the number of available detectors is limited. When assessing bat species richness at the 1-km(2) scale, the implementation of these sampling schemes at three to four forest locations yielded highest labor cost-benefit ratios but increasing equipment costs. Our study illustrates that multiple passive acoustic sampling schemes require testing based on the target taxa and habitat complexity and should be performed with reference to cost-benefit ratios. Choosing a standardized and replicated sampling scheme is particularly important to optimize the level of precision in inventories, especially when rare or elusive species are expected

Tracking marine mammals in 3D using electronic tag data

1. Information about at-depth behaviour of marine mammals is fundamental yet very hard to obtain from direct visual observation. Animal-borne multisensor electronic tags provide a unique window of observation into such behaviours. 2. Electronic tag sensors allow the estimation of the animal's 3-dimensional (3D) orientation, depth and speed. Using tag flow noise level to provide an estimate of animal speed, we extend existing approaches of 3D track reconstruction by allowing the direction of movement to differ from that of the animal's longitudinal axis. 3. Data are processed by a hierarchical Bayesian model that allows processing of multisource data, accounting for measurement errors and testing hypotheses about animal movement by comparing models. 4. We illustrate the approach by reconstructing the 3D track of a 52-min deep dive of a Blainville's beaked whale Mesoplodon densirostris adult male fit with a digital tag (DTAG) in the Bahamas. At depth, the whale alternated regular movements at large speed (>1·5 m s-1) and more complex movements at lower speed (<1·5 m s-1) with differences between movement and longitudinal axis directions of up to 28°. The reconstructed 3D track agrees closely with independent acoustic-based localizations. 5. The approach is potentially applicable to study the underwater behaviour (e.g. response to anthropogenic disturbances) of a wide variety of species of marine mammals fitted with triaxial magnetometer and accelerometer tags.PostprintPeer reviewe

Senescence and costs of reproduction in the life history of a small precocial species

Trillmich F, Geißler E, Günther A. Senescence and costs of reproduction in the life history of a small precocial species. Ecology and Evolution. 2019;9(12):7069-7079.Species following a fast life history are expected to express fitness costs mainly as increased mortality, while slow-lived species should suffer fertility costs. Because observational studies have limited power to disentangle intrinsic and extrinsic factors influencing senescence, we manipulated reproductive effort experimentally in the cavy (Cavia aperea) which produces extremely precocial young. We created two experimental groups: One was allowed continuous reproduction (CR) and the other intermittent reproduction (IR) by removing males at regular intervals. We predicted that the CR females should senesce (and die) earlier and produce either fewer and/or smaller, slower growing offspring per litter than those of the IR group. CR females had 16% more litters during three years than IR females. CR females increased mass and body condition more steeply and both remained higher until the experiment ended. Female survival showed no group difference. Reproductive senescence in litter size, litter mass, and reproductive effort (litter mass/maternal mass) began after about 600 days and was slightly stronger in CR than IR females. Litter size, litter mass, and offspring survival declined with maternal age and were influenced by seasonality. IR females decreased reproductive effort less during cold seasons and only at higher age than CR females. Nevertheless, offspring winter mortality was higher in IR females. Our results show small costs of reproduction despite high reproductive effort, suggesting that under ad libitum food conditions costs depend largely on internal regulation of allocation decisions

Different Patterns of Colonization of \u3cem\u3eOxalis alpina\u3c/em\u3e in the Sky Islands of the Sonoran Desert via Pollen and Seed Flow

Historical factors such as climatic oscillations during the Pleistocene epoch have dramatically impacted species distributions. Studies of the patterns of genetic structure in angiosperm species using molecular markers with different modes of inheritance contribute to a better understanding of potential differences in colonization and patterns of gene flow via pollen and seeds. These markers may also provide insights into the evolution of reproductive systems in plants. Oxalis alpina is a tetraploid, herbaceous species inhabiting the Sky Island region of the southwestern United States and northern Mexico. Our main objective in this study was to analyze the influence of climatic oscillations on the genetic structure of O. alpina and the impact of these oscillations on the evolutionary transition from tristylous to distylous reproductive systems. We used microsatellite markers and compared our results to a previous study using chloroplast genetic markers. The phylogeographic structure inferred by both markers was different, suggesting that intrinsic characteristics including the pollination system and seed dispersal have influenced patterns of gene flow. Microsatellites exhibited low genetic structure, showed no significant association between geographic and genetic distances, and all individual genotypes were assigned to two main groups. In contrast, chloroplast markers exhibited a strong association between geographic and genetic distance, had higher levels of genetic differentiation, and were assigned to five groups. Both types of DNA markers showed evidence of a northward expansion as a consequence of climate warming occurring in the last 10,000 years. The data from both types of markers support the hypothesis for several independent transitions from tristyly to distyly

High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests.

During the past century, systematic wildfire suppression has decreased fire frequency and increased fire severity in the western United States of America. While this has resulted in large ecological changes aboveground such as altered tree species composition and increased forest density, little is known about the long-term, belowground implications of altered, ecologically novel, fire regimes, especially on soil biological processes. To better understand the long-term implications of ecologically novel, high-severity fire, we used a 44-yr high-severity fire chronosequence in the Sierra Nevada where forests were historically adapted to frequent, low-severity fire, but were fire suppressed for at least 70 yr. High-severity fire in the Sierra Nevada resulted in a long-term (44 +yr) decrease (&gt;50%, P &lt; 0.05) in soil extracellular enzyme activities, basal microbial respiration (56-72%, P &lt; 0.05), and organic carbon (&gt;50%, P &lt; 0.05) in the upper 5 cm compared to sites that had not been burned for at least 115 yr. However, nitrogen (N) processes were only affected in the most recent fire site (4 yr post-fire). Net nitrification increased by over 600% in the most recent fire site (P &lt; 0.001), but returned to similar levels as the unburned control in the 13-yr site. Contrary to previous studies, we did not find a consistent effect of plant cover type on soil biogeochemical processes in mid-successional (10-50 yr) forest soils. Rather, the 44-yr reduction in soil organic carbon (C) quantity correlated positively with dampened C cycling processes. Our results show the drastic and long-term implication of ecologically novel, high-severity fire on soil biogeochemistry and underscore the need for long-term fire ecological experiments

Analyzing clinical trial outcomes based on incomplete daily diary reports

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/122440/1/sim6890.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/122440/2/sim6890-sup-0001-supplementary.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/122440/3/sim6890_am.pd