Phylogeography and Proline amino acid usage of Asian tiger mosquito Aedes albopictus (Skuse 1894) populations along landscape gradients in Indonesia

Asian tiger mosquito Aedes albopictus (Skuse 1894) is one of mosquito-borne vector that globally distributed including Southeast Asia. Despite its wide distributions, information on phylogeography and its determinant factors influencing A. albopictus genetic diversity and speciation is still lacking, mainly in SE Asia country. Considering this, the phylogeography of A. albopictus along with its genetic attributes in Indonesia has been assessed. The results identify that there are 2 distinct clades of A. albopictus phylogeography. First clade was related to the human-mediated dissemination. Relative Synonymous Codon Usage (RSCU) shows the TTG, CTG, GTG, ACG, GCG, and GGG codons were seldom represented. While GGA, CGA, and followed by TAT, CAT, CCT, TCT, AAC, and TTC codons were common. From a total of 60 codons, 40% codon has RSCU > 1and 21.6 % has RSCU < 1. The differences between west and east part populations can be observed in proline amino acid signaled by CCT and CCC codons. In this amino acid, east A. albopictus has higher CCC than CCT codons. Since proline is functioned to provide energy for flight, then the differences of this proline related codon among A. albopictus populations were related to the landscape variations in west and east parts of Indonesia with east parts have more rugged landscape and this condition is quite demanding for aerial animal distribution since it requires more flight energy.

belg: A Tool for Calculating Boltzmann Entropy of Landscape Gradients

Entropy is a fundamental concept in thermodynamics that is important in many fields, including image processing, neurobiology, urban planning, and sustainability. As of recently, the application of Boltzmann entropy for landscape patterns was mostly limited to the conceptual discussion. However, in the last several years, a number of methods for calculating Boltzmann entropy for landscape mosaics and gradients were proposed. We developed an R package belg as an open source tool for calculating Boltzmann entropy of landscape gradients. The package contains functions to calculate relative and absolute Boltzmann entropy using the hierarchy-based and the aggregation-based methods. It also supports input raster with missing (NA) values, allowing for calculations on real data. In this study, we explain ideas behind implemented methods, describe the core functionality of the software, and present three examples of its use. The examples show the basic functions in this package, how to adjust Boltzmann entropy values for data with missing values, and how to use the belg package in larger workflows. We expect that the belg package will be a useful tool in the discussion of using entropy for a description of landscape patterns and facilitate a thermodynamic understanding of landscape dynamics.

FracL: A Tool for Characterizing the Fractality of Landscape Gradients from a New Perspective

The past several years have witnessed much progress in landscape ecology and fractal analysis. In landscape ecology, the gradient model of landscape patterns (i.e., landscape gradient) has emerged as a new operating paradigm, where most landscape metrics do not apply because they were developed for the patch mosaic model. In the fractal analysis, a new definition of fractal has been proposed, and various new fractal metrics have been developed. This technical note aims to provide an intersection of these two lines of advance, which will further present an opportunity to advance geo-informatics by considering the latest progress in both landscape ecology and fractal analysis. We first present an overview of the new definition of fractal and all the fractal metrics developed under this new definition. Since the chief obstacle to geographers and landscape ecologists in applying these metrics is the lack of readily accessible methods for their easy computation, we then develop an integrated tool to compute them on landscape gradients. The developed tool facilitates the computation of these new fractal metrics. A case study was carried out with real-life landscape gradients, namely a digital terrain model. These new fractal metrics and the developed tool can be expected to facilitate the fractal characterization of the patterns of gradient landscapes and the understanding of landscape dynamics from a new perspective.

Properties of a Multidimensional Landscape Model for Determining Cellular Network Thermodynamics

ABSTRACTThe steady state distributions of phenotypic responses within an isogenic population of cells result from both deterministic and stochastic characteristics of biochemical networks. A biochemical network can be characterized by a multidimensional potential landscape based on the distribution of responses and a diffusion matrix of the correlated dynamic fluctuations between N-numbers of intracellular network variables. The Boltzmann H-function defines the rate of free energy dissipation of a network system and provides a framework for determining the heat associated with the nonequilibrium steady state and its network components. We conjecture that there is an upper limit to the rate of dissipative heat produced by a biological system, and we show that the dissipative heat has a lower bound. The magnitudes of the landscape gradients and the dynamic correlated fluctuations of network variables are experimentally accessible, and through an analysis that we refer to as Thermo-Fokker-Planck (Thermo-FP), provide insight into the composition of the network and the relative thermodynamic contributions from network components. We surmise that these thermodynamic quantities allow determination of the relative importance of network components to overall network control.

Advances in Understanding Landscape Influences on Freshwater Habitats and Biological Assemblages

<i>Abstract.</i>—Linking landscape features, both natural and human-altered, to aquatic ecosystem structure and function is a fundamental objective in landscape ecology and freshwater science, but this process is data- and resource-intensive. Quantifying how landscape stressors influence aquatic communities requires balancing logistic and financial constraints with effectively sampling the landscape to capture gradients of interest. There are a variety of ways to balance these constraints, such as using existing data, handpicked site selection, or a statistical site-selection scheme. Poor sampling design reduces statistical power; however, we do not know how differences in site-selection designs influence our ability to measure ecological responses to landscape gradients. We quantified how the distribution of sample sites across landscape gradients affected the measured responses of stream fish assemblages to these gradients at different sample sizes. Specifically, we used randomization tests to compare the variability in the responses of fish assemblage structure (species richness and composition) to catchment area and land use (agricultural land) with manipulated distributions (random, highly skewed, and uniform) of sites across these landscape gradients. Assemblage composition was more sensitive than species richness to sampling design, and we observed less variability in the detected response of assemblage composition when samples were distributed uniformly across landscape gradients, especially when sample sizes were small. Although strong responses to environmental gradients, such as species richness to catchment area, are robust to sampling distributions, large sample size and a uniform distribution of samples might help elucidate more subtle responses to environmental gradients.