Fine-scale Spatial Distributions Research Articles

Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity.

Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km2 temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Metabarcoding is (usually) more cost effective than seining or qPCR for detecting tidewater gobies and other estuarine fishes.

Many studies have shown that environmental DNA (eDNA) sampling can be more sensitive than traditional sampling. For instance, past studies found a specific qPCR probe of a water sample is better than a seine for detecting the endangered northern tidewater goby, Eucyclogobius newberryi. Furthermore, a metabarcoding sample often detects more fish species than a seine detects. Less consideration has been given to sampling costs. To help managers choose the best sampling method for their budget, I estimated detectability and costs per sample to compare the cost effectiveness of seining, qPCR and metabarcoding for detecting endangered tidewater gobies as well as the associated estuarine fish community in California. Five samples were enough for eDNA methods to confidently detect tidewater gobies, whereas seining took twice as many samples. Fixed program costs can be high for qPCR and seining, whereas metabarcoding had high per-sample costs, which led to changes in relative cost-effectiveness with the number of locations sampled. Under some circumstances (multiple locations visited or an already validated assay), qPCR was a bit more cost effective than metabarcoding for detecting tidewater gobies. Under all assumptions, seining was the least cost-effective method for detecting tidewater gobies or other fishes. Metabarcoding was the most cost-effective sampling method for multiple species detection. Despite its advantages, metabarcoding has gaps in sequence databases, can yield vague results for some species, and can lead novices to serious errors. Seining remains the only way to rapidly assess densities, size distributions, and fine-scale spatial distributions.

Environmental factors associated with silver carp presence and relative abundance near an invasion front to inform removal efforts

Management of invasive fishes has relied heavily upon understanding their spatial distributions and habitat use at fine spatial scales to guide treatments and removals. In the USA, targeted removal is used in management of bigheaded carps (Hypophthalmichthys spp.) in the Mississippi River system to reduce invasion potential into the Laurentian Great Lakes from the upper Illinois Waterway. Our study tested factors linked to fine-scale spatial distributions of the most prevalent bigheaded carp species—silver carp (Hypophthalmichthys molitrix)—in the upper Illinois River to increase effectiveness of removal efforts. Bi-monthly mobile hydroacoustic sampling was conducted from 2017 to 2018 and paired with continuous environmental data collection in the two northern-most invaded reaches of the upper Illinois River. Model selection was used to describe habitat conditions associated with silver carp presence and density. Depth was the most consistent predictor of silver carp presence and density, with shallower depths consistently associated with higher abundance. During summer months, shallow areas in large backwater habitats with lower temperature and higher dissolved oxygen concentration held more silver carp. These results may help managers focus targeted removal efforts through time, increase harvest effectiveness, and reduce the potential for further invasion toward the Laurentian Great Lakes.

Models of the fine-scale spatial distributions of trees in managed and unmanaged forest patches with Abies alba Mill. and Fagus sylvatica L.

Fine-scale spatial point-pattern analysis can give insights into the underlying pattern-creating biological processes in an environmental context. However, there are few studies comparing the spatial distribution of trees in managed stands and unmanaged forests that take into account their developmental stage. The main aim of this study was to assess and model the spatial patterns of Abies alba Mill. and Fagus sylvatica L. trees in managed and unmanaged forest patches in the early developmental stage.This study investigated tree communities dominated by A. alba and F. sylvatica in the Świętokrzyskie Mountains in Central Europe. From 2016 to 2018, 60 sample plots representing the growing-up developmental stage were randomly selected: 30 from managed stands and 30 from unmanaged forests. Models of the fine-scale spatial distributions of the trees were distinguished using hierarchical cluster analysis (HCA), analysis of group similarities (ANOSIM), and multiple response permutation procedures (MRPP). Indices based on the K-function and the O-ring statistic, ILr and IOr, respectively, were developed and used as clustering variables. The proposed indices assume values from −1 to 1 for random patterns; values > 1 indicate aggregation, and values < −1 indicate regularity.Models of the fine-scale spatial distributions of the trees differed only slightly between the managed and unmanaged patches. These models suggest that in the investigated sample plots, the fine-scale spatial patterns (with distances among the trees not exceeding 10 m) were usually random. Only in a few patches were the tree distributions found to be aggregated, from 5 to 10 m and from 7 to 10 m in the managed stands and the unmanaged forests, respectively. The relatively similar models of the fine-scale spatial distributions of the trees in the managed and unmanaged forest patches in the growing-up developmental stage show that early successional forest dynamics follow a parallel trajectory of recovery. The long-term application of the shelterwood system as well as self-regeneration and self-regulation natural processes led to the creation of the similar spatial structures of the trees. This observation may be helpful in the design of planting patterns and/or harvesting schedules.

A three-dimensional spatial mapping approach to quantify fine-scale heterogeneity among leaves within canopies.

Premise of the study:The three-dimensional structure of tree canopies creates environmental heterogeneity, which can differentially influence the chemistry, morphology, physiology, and/or phenology of leaves. Previous studies that subdivide canopy leaves into broad categories (i.e., “upper/lower”) fail to capture the differences in microenvironments experienced by leaves throughout the three-dimensional space of a canopy.Methods:We use a three-dimensional spatial mapping approach based on spherical polar coordinates to examine the fine-scale spatial distributions of photosynthetically active radiation (PAR) and the concentration of ultraviolet (UV)-absorbing compounds (A300) among leaves within the canopies of black mangroves (Avicennia germinans).Results:Linear regressions revealed that interior leaves received less PAR and produced fewer UV-absorbing compounds than leaves on the exterior of the canopy. By allocating more UV-absorbing compounds to the leaves on the exterior of the canopy, black mangroves may be maximizing UV-protection while minimizing biosynthesis of UV-absorbing compounds.Discussion:Three-dimensional spatial mapping provides an inexpensive and portable method to detect fine-scale differences in environmental and biological traits within canopies. We used it to understand the relationship between PAR and A300, but the same approach can also be used to identify traits associated with the spatial distribution of herbivores, pollinators, and pathogens.

Predicting Variation in Microhabitat Utilization of Terrestrial Salamanders

Understanding patterns of microhabitat use among terrestrial salamanders is important for predicting their responses to natural and anthropogenic disturbances. The dependence of terrestrial salamanders on cutaneous respiration limits their spatial distribution to moist, humid areas. Although many studies have shown negative effects of canopy removal on terrestrial salamander abundance, some have shown potential ameliorating effects of retaining coarse woody debris (CWD) as moist refugia (critical resources in the landscape). Because cover objects like CWD retain moisture longer than fine debris, terrestrial salamanders are often more locally abundant in areas of dense cover. Temporally variable environmental conditions could affect microhabitat quality and influence the fine-scale spatial distributions of salamanders. Spatial and temporal variability in microhabitat use greatly influence individual detectability, which is always a challenge for terrestrial salamanders. We conducted repeated area-constrained surveys to examine variation in salamander microhabitat use of terrestrial salamanders in relation to season, year, and weather conditions. We found that time since rain (TSR) was the best predictor of relative salamander microhabitat use, but the strength of this relationship varied among years. In addition, TSR was also the best predictor of salamander surface activity. We captured most salamanders within leaf litter, but the proportion of leaf litter captures varied with TSR. Our results illustrate the importance of accounting for variable detectability when sampling for terrestrial salamanders. Disturbances which affect leaf litter depth and decomposition rates could influence the availability and quality of microhabitats and potentially increase competition among individuals for natural cover objects.

Revisiting the use of seismic attributes as soft data for subseismic facies prediction: Proportions versus probabilities

Geostatistical modeling originated within the mining industry to estimate average minable ore grade from large support volumes given samples measured on small volume support. In petroleum geostatistics, the goal is more equivocal due to several different scales of support of input data, which are often incongruent with the desired prediction scale. More specifically, the goal is to utilize indirect measurements (e.g., seismic data) from a scale larger than the prediction scale for fine-scale spatial distributions of facies and petrophysical properties grounded by undersampled point data (e.g., well-log data). (Note, volume support is a geostatistical term that describes the size or resolution of the sample or measurement.)

The Influence of Maternal Lineages on Social Affiliations among Humpback Whales (Megaptera novaeangliae) on Their Feeding Grounds in the Southern Gulf of Maine

Humpback whales on their feeding grounds in the Gulf of Maine typically form fluid fission/fusion groups of two to three individuals characterized by noncompetitive and, at times, cooperative behavior. Here we test the hypothesis that, despite the apparent absence of close kinship bonds, the fluid associations between feeding whales are influenced by "maternal lineages" as represented by mtDNA haplotypes. Using skin samples collected with a biopsy dart, variation in the hypervariable segment of the mtDNA control region identified 17 unique haplotypes among 159 individually identified whales from the southern Gulf of Maine. The haplotypes of a further 143 individuals were inferred from known direct maternal (cow-calf) relationships. The frequencies of associations among these 302 individuals were calculated from 21,617 sighting records collected from 1980 to 1995, excluding associations between a cow and her dependent calf. For groups of two where the haplotypes of both individuals were known (n = 3,151), individuals with the same haplotype were together significantly more often (26%) than expected by random association (20%). To account for different group sizes and associations with individuals of unknown haplotype and sex, we used Monte Carlo simulations to test for nonrandom associations in the full data set, as well as known female-only (n = 1,512), male-only (n = 730), and mixed-sex (n = 2,745) groups. Within-haplotype associations were significantly more frequent than expected at random for all groups (P = .002) and female-only groups (P = .011) but not male-only groups, while mixed-sex groups approached significance (P = .062). A Mantel test of individual pairwise association indices and haplotype identity confirmed that within-haplotype associations were more frequent than expected for all sex combinations except male-male associations, with females forming within-haplotype associations 1.7 times more often than expected by random assortment. Partial matrix correlations and permutation analyses indicated that the skew toward within-haplotype associations could not be accounted for by short-term temporal co-occurrence or fine-scale spatial distributions of individuals with shared haplotypes. While the mechanism by which individuals with a common mtDNA haplotype assort remains unknown, our results strongly suggest an influence of maternal lineages on the social organization of humpback whales within a regional feeding ground.

A Large-Volume Pump System for Studies of the Vertical Distribution of Fish Larvae Under Open Sea Conditions

A large-volume pump system (2.8 m3 min-1) for sampling fish larvae under open-sea conditions is described. Comparative efficiency trials by day and night showed that the pump was generally as efficient, or in some cases more efficient, in capturing larvae than vertically hauled 200 μm WP2 nets, though there was some evidence of visual avoidance by particular larval size classes during daylight. The pump system is particularly appropriate for investigating fine-scale vertical aggregations (1–10 m3) of larval fish in relation to the distribution of their food organisms.INTRODUCTIONStudies of the distribution of larval fish and their food organisms in relation to physical structure in the water column require sampling techniques capable of resolving fine-scale temporal and spatial distributions. As an alternative to conventional nets, large-volume pumps, sampling at rates in excess of 1 m3 min-1; provide such a capability. Major benefits of using large pumps in addition to temporal and spatial resolution are that a wide range of sizes of plankton including larval fish can be sampled simultaneously in relation to physical and chemical properties of the water column; there is reliable control of the volume of sample filtered and problems of clogging of towed nets are avoided; long series of sequential samples can be taken in studies of small-scale distribution; and instrumentation with in situ CTD and fluorometers at the intake enables real-time control of sampling in relation to physical structure.General engineering considerations for using such pumps have been reviewed in detail by Miller &amp; Judkins (1981), and a particular area of application has been in power-plant entrainment studies in shallow fresh water (Portner &amp; Rhode, 1977; Bowles &amp; Merriner, 1978; Gale &amp; Mohr, 1978; Ney &amp; Schumacher, 1978; Elder et al. 1979; Leithiser, Ehrlich &amp; Thum, 1979; Cada &amp; Loar, 1982).