Underdispersion models: Models that are “under the radar”

Sellers, Kimberly F.; Morris, Darcy Steeg

doi:10.1080/03610926.2017.1291976

Cited by 36 publications

(24 citation statements)

References 28 publications

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“…We tested differences in microhabitat numbers and occurrences between living and dead trees with post-hoc multi-comparison Tukey tests for a fixed mean DBH (44 cm; function cld, library emmeans [27]). Dispersion diagnostics revealed under-dispersed model estimations, which may cause a type II error rate inflation [28]. However, since there was no simple way to account for that in a frequentist framework, we kept the results while bearing in mind that they were undoubtedly conservative despite the large number of observations we analysed.…”

Section: Methodsmentioning

confidence: 99%

Nothing else matters? Tree diameter and living status have more effects than biogeoclimatic context on microhabitat number and occurrence: An analysis in French forest reserves

Paillet

Debaive²,

Archaux

et al. 2019

PLoS ONE

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Managing forests to preserve biodiversity requires a good knowledge not only of the factors driving its dynamics but also of the structural elements that actually support biodiversity. Tree-related microhabitats (e.g. cavities, cracks, conks of fungi) are tree-borne features that are reputed to support specific biodiversity for at least a part of species’ life cycles. While several studies have analysed the drivers of microhabitats number and occurrence at the tree scale, they remain limited to a few tree species located in relatively narrow biogeographical ranges. We used a nationwide database of forest reserves where microhabitats were inventoried on more than 22,000 trees. We analysed the effect of tree diameter and living status (alive or dead) on microhabitat number and occurrence per tree, taking into account biogeoclimatic variables and tree genus. We confirmed that larger trees and dead trees bore more microhabitats than their smaller or living counterparts did; we extended these results to a wider range of tree genera and ecological conditions than those studied before. Contrary to our expectations, the total number of microhabitat types per tree barely varied with tree genus–though we did find slightly higher accumulation levels for broadleaves than for conifers–nor did it vary with elevation or soil pH, whatever the living status. We observed the same results for the occurrence of individual microhabitat types. However, accumulation levels with diameter and occurrence on dead trees were higher for microhabitats linked with wood decay processes (e.g. dead branches or woodpecker feeding holes) than for other, epixylic, microhabitats such as epiphytes (ivy, mosses and lichens). Promoting large living and dead trees of several tree species may be a relevant, and nearly universal, way to favour microhabitats and enhance the substrates needed to support specific biodiversity. In the future, a better understanding of microhabitat drivers and dynamics at the tree scale may help to better define their role as biodiversity indicators for large-scale monitoring.

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Section: Methodsmentioning

confidence: 99%

Nothing else matters? Tree diameter and living status have more effects than biogeoclimatic context on microhabitat number and occurrence: An analysis in French forest reserves

Paillet

Debaive²,

Archaux

et al. 2019

PLoS ONE

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show abstract

“…However, there is indirect evidence for such interference effects, from estimates of the extent of underdispersion of the numbers of adaptive substitutions observed over the last 8N generations of the simulations compared with the expectation for a Poisson distribution, as described in File S1, section S8. Here, underdispersion is measured by the ratio of the variance to the mean of the number of substitutions over the period of observation (Sellers and Morris 2017).…”

Section: Effects Of Interference Among Favorable Mutations On Their Rmentioning

confidence: 99%

The Effects on Neutral Variability of Recurrent Selective Sweeps and Background Selection

Campos

Charlesworth

2019

Genetics

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Levels of variability and rates of adaptive evolution may be affected by hitchhiking, the effect of selection on evolution at linked sites. Hitchhiking can be caused either by "selective sweeps" or by background selection, involving the spread of new favorable alleles or the elimination of deleterious mutations, respectively. Recent analyses of population genomic data have fitted models where both these processes act simultaneously, to infer the parameters of selection. Here, we investigate the consequences of relaxing a key assumption of some of these studies, that the time occupied by a selective sweep is negligible compared with the neutral coalescent time. We derive a new expression for the expected level of neutral variability in the presence of recurrent selective sweeps and background selection. We also derive approximate integral expressions for the effects of recurrent selective sweeps. The accuracy of the theoretical predictions was tested against multilocus simulations, with selection, recombination, and mutation parameters that are realistic for Drosophila melanogaster. In the presence of crossing over, there is approximate agreement between the theoretical and simulation results. We show that the observed relationships between the rate of crossing over, and the level of synonymous site diversity and rate of adaptive evolution in Drosophila are probably mainly caused by background selection, whereas selective sweeps and population size changes are needed to produce the observed distortions of the site frequency spectrum.

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“…Differences of microhabitats number and occurrences between living and dead trees were tested using post-hoc multicomparison Tukey tests for a fixed mean DBH (44cm; function cld, library emmeans [27]). Dispersion diagnostics revealed underdispersed model estimations, which may cause a type II error rate inflation [28]. However, since there was no simple way to account for that in a frequentist framework, we kept with these results, bearing in mind that our results were conservative despite the large number of observations we analysed.…”

Section: Methodsmentioning

confidence: 99%

Nothing else matters? Tree characteristics have more effects than biogeoclimatic context on microhabitat diversity and occurrence: a nationwide analysis

Paillet

Debaive²,

Archaux

et al. 2018

Preprint

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16Managing forests to preserve biodiversity requires a good knowledge not only of the factors 17 driving its dynamics but also of the structural elements that actually support biodiversity. Tree-18 related microhabitats (cavities, cracks, conks of fungi) are tree-borne features that are reputed 19 to support specific biodiversity for at least a part of species' life cycles. While several studies 20 have analysed the drivers of microhabitats number and occurrence at the tree scale, they 21 remain limited to a few tree species located in relatively narrow biogeographical ranges. We 22Promoting large living and dead trees of several tree species may be an interesting, and nearly 36 universal, way to favour microhabitats and enhance the substrates needed to support specific 37 biodiversity. In addition, a better understanding of microhabitat drivers and dynamics at the 38 tree scale may help to better define their role as biodiversity indicators for large-scale 39 monitoring. 40 41 42 Small natural features are structural habitat elements that have a disproportionately important 43 role for biodiversity related to their actual size [1]. Taking these features into account in 44 biodiversity conservation strategies is a crucial step in science-based decision making [2]. 45Identifying such structural features in a tri-dimensional forest environment is quite challenging 46 since their number and variety is potentially infinite. Small natural features include, for example, 47 large old trees [3] as well as tree-borne structures. While large old trees are disappearing at 48 the global scale [4], their importance for biodiversity has not yet been fully elucidated, not to 49 mention the peculiar structures they may bear (eg. cracks, cavities, epiphytes), also known as 50 'tree-related microhabitats' (hereafter 'microhabitats' [5]). Microhabitats have recently aroused 51 the interest of scientists and forest managers alike since these structures can be a substrate 52for specific forest biodiversity [6], and can ultimately serve as forest biodiversity indicators [5, 53 7, 8]. Their conservation has hence become an issue in day-to-day forest management, as 54 have large old trees and deadwood [9, 10]. However, our understanding of the drivers and 55 dynamics influencing these microhabitats, notably at the tree scale, remains incomplete [11]. 56Tree diameter and living status (living vs. dead trees) are key factors for microhabitat diversity 57 at the tree scale [12][13][14]. Larger trees are likely to bear more microhabitats than smaller ones, 58as they have experienced more damage, injuries and microhabitat-creating events (e.g. 59 woodpecker excavation, storms, snowfalls). Similarly, gradually decomposing dead trees are 60 likely to bear more microhabitats than living trees and play a role as habitat and food sources 61 for many microhabitat-creating species [15]. Nevertheless, the relationships between 62 microhabitats and tree characteristics have only been demonstrated on a limited number of 63 tree species involving at...

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Underdispersion models: Models that are “under the radar”

Cited by 36 publications

References 28 publications

Nothing else matters? Tree diameter and living status have more effects than biogeoclimatic context on microhabitat number and occurrence: An analysis in French forest reserves

Nothing else matters? Tree diameter and living status have more effects than biogeoclimatic context on microhabitat number and occurrence: An analysis in French forest reserves

The Effects on Neutral Variability of Recurrent Selective Sweeps and Background Selection

Nothing else matters? Tree characteristics have more effects than biogeoclimatic context on microhabitat diversity and occurrence: a nationwide analysis

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