The<b>ecodist</b>Package for Dissimilarity-based Analysis of Ecological Data

Goslee, Sarah C.; Urban, Dean L.

doi:10.18637/jss.v022.i07

Cited by 2,146 publications

(1,650 citation statements)

References 32 publications

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“…We evaluated all data for normality by generating box-and-whisker, histogram and quantile-quantile plots and log-transformed data when necessary. We explored relationships between gas flux and potential explanatory variables using the Ecodist package (Goslee and Urban 2007) and by building generalized linear models (GLM). We used these models to estimate daily emissions of CO 2 and CH 4 and generate an annual flux budget from March 1, 2012 to February 28, 2013.…”

Section: Statistical Analysesmentioning

confidence: 99%

The Effects of Organic Matter Amendments on Greenhouse Gas Emissions from a Mitigation Wetland in Virginia’s Coastal Plain

Winton

Richardson

2015

Wetlands

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There is concern that widespread restoration and/or creation of freshwater wetlands may present a radiative forcing hazard because of the potential for methane (CH 4 ) emissions. Yet data on greenhouse gas (GHG) emissions from restored wetlands are sparse and there has been little investigation into the GHG effects of amending wetland soils with organic matter (OM), a practice used to improve function of mitigation wetlands in the Eastern United States. In this study we measure GHG emissions across an OM gradient at the Charles City Wetland (CCW) in Charles City County, Virginia. We found soils heavily loaded with OM emit significantly more CO 2 than those that have received little or no OM. CH 4 emissions from CCW are low compared to reference wetlands and show no relationship with the loading rate of added OM or total soil carbon. We conclude that adding moderate amounts (<~150 kg m −2 ) of OM to the CCW does not greatly increase GHG emissions, while the addition of high amounts of OM produces additional CO 2 , but not CH 4 . CH 4 flux is highest under flooded conditions during warmer months but it still a modest contribution to global warming potential compared to soil CO 2 flux.

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Section: Statistical Analysesmentioning

confidence: 99%

The Effects of Organic Matter Amendments on Greenhouse Gas Emissions from a Mitigation Wetland in Virginia’s Coastal Plain

Winton

Richardson

2015

Wetlands

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“…We compared the two matrices in a Mantel test with 10,000 permutations to evaluate the level of significance for the Pearson correlation coefficient in package ecodist (Goslee & Urban, 2007).…”

Section: Isolation-by-distancementioning

confidence: 99%

Habitat fragmentation has interactive effects on the population genetic diversity and individual behaviour of a freshwater salmonid fish

Leeuwen

Dalen

Museth

et al. 2017

River Research & Apps

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Sufficient genetic diversity can aid populations to persist in dynamic and fragmented environments. Understanding which mechanisms regulate genetic diversity of riverine fish can therefore advance current conservation strategies. The aim of this study was to investigate how habitat fragmentation interacted with population genetic diversity and individual behaviour of freshwater fish in large river systems. We studied a population of the long-distance migratory, iteroparous freshwater salmonid European grayling (Thymallus thymallus) in south-eastern Norway. Genotyping (n = 527) and radio-tracking (n = 54) of adult fish throughout a 169-km river section revealed three major migration barriers limiting gene flow and depleting genetic diversity upstream. Individuals from upstream areas that had dispersed downstream of barriers showed different movement behaviour than local genotypes. No natal philopatry was found in a large unfragmented river section, in contrast to strong fidelity to spawning tributaries known for individuals overwintering in lakes. We conclude that (a) upstream sub-populations in fragmented rivers show less genetic variation, making it less likely for them to adapt to environmental changes; (b) fish with distinct genotypes in the same habitat can differ in their behaviour; (c) spawning site selection (natal philopatry) can differ between fish of the same species living in different habitats.Together this implies that habitat loss and fragmentation may differently affect individual fish of the same species if they live in different types or sections of habitat. Studying behaviour and genetic diversity of fish can unravel their complex ecology and help minimize human impact.

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“…We examined the association between geographical distance and genetic divergence (isolation by distance, IBD) with a Mantel test using the package Ecodist 1.1.3 (Goslee and Urban 2007) in the software R 2.12.2 (R Development Core Team 2011), using 10,000 permutations, and bootstrapping confidence limits with 1,000 iterations. Genetic divergence was measured as F ST /(1 -F ST ), and geographic distances between sample sites were calculated as shortest waterway distance using ArcGIS 10 (ESRI 2010, Redlands, CA, USA).…”

Section: Association Between Geographical Distance and Genetic Divergmentioning

confidence: 99%

Genetic biodiversity in the Baltic Sea: species-specific patterns challenge management

et al. 2013

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Information on spatial and temporal patterns of genetic diversity is a prerequisite to understanding the demography of populations, and is fundamental to successful management and conservation of species. In the sea, it has been observed that oceanographic and other physical forces can constitute barriers to gene flow that may result in similar population genetic structures in different species. Such similarities among species would greatly simplify management of genetic biodiversity. Here, we tested for shared genetic patterns in a complex marine area, the Baltic Sea. We assessed spatial patterns of intraspecific genetic diversity and differentiation in seven ecologically important species of the Baltic ecosystem-Atlantic herring (Clupea harengus), northern pike (Esox lucius), European whitefish (Coregonus lavaretus), three-spined stickleback (Gasterosteus aculeatus), nine-spined stickleback (Pungitius pungitius), blue mussel (Mytilus spp.), and 123Biodivers Conserv ( ) 22:3045-3065 DOI 10.1007 bladderwrack (Fucus vesiculosus). We used nuclear genetic data of putatively neutral microsatellite and SNP loci from samples collected from seven regions throughout the Baltic Sea, and reference samples from North Atlantic areas. Overall, patterns of genetic diversity and differentiation among sampling regions were unique for each species, although all six species with Atlantic samples indicated strong resistence to Atlantic-Baltic gene-flow. Major genetic barriers were not shared among species within the Baltic Sea; most species show genetic heterogeneity, but significant isolation by distance was only detected in pike and whitefish. These species-specific patterns of genetic structure preclude generalizations and emphasize the need to undertake genetic surveys for species separately, and to design management plans taking into consideration the specific structures of each species.

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TheecodistPackage for Dissimilarity-based Analysis of Ecological Data

Cited by 2,146 publications

References 32 publications

The Effects of Organic Matter Amendments on Greenhouse Gas Emissions from a Mitigation Wetland in Virginia’s Coastal Plain

The Effects of Organic Matter Amendments on Greenhouse Gas Emissions from a Mitigation Wetland in Virginia’s Coastal Plain

Habitat fragmentation has interactive effects on the population genetic diversity and individual behaviour of a freshwater salmonid fish

Genetic biodiversity in the Baltic Sea: species-specific patterns challenge management

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