scholarly journals Current nest box designs may not be optimal for the larger forest dormice: Pre‐hibernation increase in body mass might lead to sampling bias in ecological data

2021 ◽  
Author(s):  
Hesamaddin Farhadi
Keyword(s):  
Body Mass ◽  
Sampling Bias ◽  
Ecological Data ◽  
Nest Box

scholarly journals Macroecological analyses support an overkill scenario for late Pleistocene extinctions

2004 ◽  
Vol 64 (3a) ◽  
pp. 407-414 ◽  
Author(s):  
J. A. F. Diniz-Filho
Keyword(s):  
Body Mass ◽  
Population Dynamic ◽  
High Selectivity ◽  
Environmental Changes ◽  
Dynamic Parameters ◽  
Allometric Relationships ◽  
Ecological Data ◽  
Predator Prey ◽  
A Value ◽  
Complex Models

The extinction of megafauna at the end of Pleistocene has been traditionally explained by environmental changes or overexploitation by human hunting (overkill). Despite difficulties in choosing between these alternative (and not mutually exclusive) scenarios, the plausibility of the overkill hypothesis can be established by ecological models of predator-prey interactions. In this paper, I have developed a macroecological model for the overkill hypothesis, in which prey population dynamic parameters, including abundance, geographic extent, and food supply for hunters, were derived from empirical allometric relationships with body mass. The last output correctly predicts the final destiny (survival or extinction) for 73% of the species considered, a value only slightly smaller than those obtained by more complex models based on detailed archaeological and ecological data for each species. This illustrates the high selectivity of Pleistocene extinction in relation to body mass and confers more plausibility on the overkill scenario.

scholarly journals Phylofactorization: a graph-partitioning algorithm to identify phylogenetic scales of ecological data

2017 ◽  
Author(s):  
Alex D. Washburne ◽  
Justin D. Silverman ◽  
James T. Morton ◽  
Daniel J. Becker ◽  
Daniel Crowley ◽  
...  
Keyword(s):  
Body Mass ◽  
Graph Partitioning ◽  
R Package ◽  
Ecological Groups ◽  
Reduced Rank Regression ◽  
Ecological Data ◽  
Phylogenetic Constraint ◽  
Partitioning Algorithm ◽  
Relative Abundances ◽  
Additive Modeling

AbstractThe problem of pattern and scale is a central challenge in ecology. The problem of scale is central to community ecology, where functional ecological groups are aggregated and treated as a unit underlying an ecological pattern, such as aggregation of “nitrogen fixing trees” into a total abundance of a trait underlying ecosystem physiology. With the emergence of massive community ecological datasets, from microbiomes to breeding bird surveys, there is a need to objectively identify the scales of organization pertaining to well-defined patterns in community ecological data.The phylogeny is a scaffold for identifying key phylogenetic scales associated with macroscopic patterns. Phylofactorization was developed to objectively identify phylogenetic scales underlying patterns in relative abundance data. However, many ecological data, such as presence-absences and counts, are not relative abundances, yet it is still desireable and informative to identify phylogenetic scales underlying a pattern of interest. Here, we generalize phylofactorization beyond relative abundances to a graph-partitioning algorithm for any community ecological data.Generalizing phylofactorization connects many tools from data analysis to phylogenetically-informe analysis of community ecological data. Two-sample tests identify three phylogenetic factors of mammalian body mass which arose during the K-Pg extinction event, consistent with other analyses of mammalian body mass evolution. Projection of data onto coordinates defined by the phylogeny yield a phylogenetic principal components analysis which refines our understanding of the major sources of variation in the human gut microbiome. These same coordinates allow generalized additive modeling of microbes in Central Park soils and confirm that a large clade of Acidobacteria thrive in neutral soils. Generalized linear and additive modeling of exponential family random variables can be performed by phylogenetically-constrained reduced-rank regression or stepwise factor contrasts. We finish with a discussion of how phylofac-torization produces an ecological species concept with a phylogenetic constraint. All of these tools can be implemented with a new R package available online.

scholarly journals ‘SRS’ R Package and ‘q2-srs’ QIIME 2 Plugin: Normalization of Microbiome Data Using Scaling with Ranked Subsampling (SRS)

2021 ◽  
Vol 11 (23) ◽  
pp. 11473
Author(s):  
Vitor Heidrich ◽  
Petr Karlovsky ◽  
Lukas Beule
Keyword(s):  
Community Structure ◽  
Count Data ◽  
Sampling Bias ◽  
R Package ◽  
Data Types ◽  
Ecological Data ◽  
Technical Artifacts ◽  
Microbiome Data

Several ecological data types, especially microbiome count data, are commonly sample-wise normalized before analysis to correct for sampling bias and other technical artifacts. Recently, we developed an algorithm for the normalization of ecological count data called ‘scaling with ranked subsampling (SRS)’, which surpasses the widely adopted ‘rarefying’ (random subsampling without replacement) in reproducibility and in safeguarding the original community structure. Here, we describe an implementation of the SRS algorithm in the ‘SRS’ R package and the ‘q2-srs’ QIIME 2 plugin. We also provide accessory functions for dataset exploration to guide the choice of parameters for SRS.

Sampling bias affects the relationship between structural importance and species body mass in frugivore-plant interaction networks

2020 ◽  
Vol 44 ◽  
pp. 100870
Author(s):  
Juan Fernando Acevedo-Quintero ◽  
Romeo A. Saldaña-Vázquez ◽  
Eduardo Mendoza ◽  
Joan Gastón Zamora-Abrego
Keyword(s):  
Body Mass ◽  
Sampling Bias ◽  
Interaction Networks ◽  
Plant Interaction ◽  
Structural Importance ◽  
The Relationship

scholarly journals Pitfall trap sampling bias depends on body mass, temperature, and trap number: insights from an individual‐based model

Ecosphere ◽  
2017 ◽  
Vol 8 (4) ◽  
Author(s):  
Jan Engel ◽  
Lionel Hertzog ◽  
Julia Tiede ◽  
Cameron Wagg ◽  
Anne Ebeling ◽  
...  
Keyword(s):  
Body Mass ◽  
Sampling Bias ◽  
Pitfall Trap ◽  
Individual Based Model ◽  
Mass Temperature

scholarly journals Thermal Environment of the Nest During Development of Tree Swallow (Tachycineta bicolor) Chicks

The Auk ◽  
2002 ◽  
Vol 119 (3) ◽  
pp. 845-851
Author(s):  
Susan B. Chaplin ◽  
Mora L. Cervenka ◽  
Alison C. Mickelson
Keyword(s):  
Regression Analysis ◽  
Body Mass ◽  
Brood Size ◽  
Thermal Environment ◽  
Tachycineta Bicolor ◽  
Tree Swallow ◽  
East Central ◽  
Nest Box

Abstract We continuously recorded temperatures of the nest cup (Tn) and air (Ta) just outside the nest box throughout development of Tree Swallow (Tachycineta bicolor) chicks in east-central Minnesota. Brood size was manipulated (three or six chicks per nest) to study the effect of number of chicks in the nest on its thermal environment. From day 0 to day 4, Tn paralleled Ta, approximately 2–7°C higher, with nocturnal Tn maintained at 24°C and daytime Tn maintained at 26°C. From day 6 to day 12, Tn was relatively constant throughout the day, maintained at 32°C (day) and 29°C (night). The Tn became increasingly independent of Ta, as determined by regression analysis of Tn versus Ta with age. Nocturnal Tn of larger clutches (six chicks) was ∼2°C warmer than smaller clutches (three chicks), and Tn of larger clutches exhibited greater independence from Ta at day 10 than in smaller clutches. The occurrence of nest homeothermy at day 10 in six-chick nests correlates with near-maximal body mass of chicks and completion of feather insulation. Small (three-chick) clutches showed greater dependence of Tn on Ta at 10–12 days of age than large (six-chick) clutches; we propose that development of thermoregulatory capacity may have proceeded more slowly in chicks from those nests.

A review of terrestrial mammalian and reptilian carnivore ecology in Australian fossil faunas, and factors influencing their diversity: the myth of reptilian domination and its broader ramifications

2002 ◽  
Vol 50 (1) ◽  
pp. 1 ◽  
Author(s):  
S. Wroe
Keyword(s):  
Species Richness ◽  
Body Mass ◽  
Species Abundance ◽  
Biological Significance ◽  
Nutrient Deficiency ◽  
Soil Nutrient ◽  
Sampling Bias ◽  
Quantitative Methodology ◽  
Prima Facie Case ◽  
Extant Species

The notion that Australia’s large, terrestrial carnivore faunas of the middle Tertiary to Pleistocene were dominated by reptiles has gained wide acceptance in recent decades. Simple but sweeping hypotheses have been developed seeking to explain this perceived ecological phenomenon. However, a review of the literature does not support these interpretations, which are based on largely speculative and, in many cases, clearly erroneous assumptions. Few size estimates of fossil reptilian taxa are based on quantitative methodology and, regardless of method, most are restricted to maximum dimensions. For species of indeterminate growth, this practice generates misleading perceptions of biological significance. In addition to misconceptions with respect to size, much speculation concerning the lifestyles of large extinct reptiles has been represented as fact. In reality, it has yet to be demonstrated that the majority of fossil reptiles underpinning the story of reptilian domination were actually terrestrial. No postcranial evidence suggests that any Australian mekosuchine crocodylian was less aquatic than extant species, while a semi-aquatic habitus has been posited for madtsoiid snakes and even the giant varanid, Megalania. Taphonomic data equivocally supports the hypothesis that some Australian mekosuchines were better adapted to life on land than are most extant crocodylians, but still semi-aquatic and restricted to the near vicinity of major watercourses. On the other hand, the accelerating pace of discovery of new large mammalian carnivore species has undermined any prima facie case for reptilian supremacy regarding pre-Pleistocene Australia (that is, if species richness is to be used as a gauge of overall impact). However, species abundance and consumption, not richness, are the real measures. On this basis, even in Pleistocene Australia, where species richness of large mammalian carnivores was relatively low, available data expose the uncommon and geographically restricted large contemporaneous reptiles as bit players. In short, the parable of a continent subject to a Mesozoic rerun, wherein diminutive mammals trembled under the footfalls of a menagerie of gigantic ectotherms, appears to be a castle in the air. However, there may be substance to some assertions. Traditionally, erratic climate and soil-nutrient deficiency have been invoked to explain the perception of low numbers or relatively small sizes of fossil mammalian carnivore taxa in Australia. But these arguments assume a simple and positive relationship between productivity, species richness and maximum body mass and either fail to recognise, or inappropriately exclude, other factors. Productivity has undoubtedly played a role, but mono-factorial paradigms cannot account for varying species richness and body mass among Australia’s fossil faunas. Nor can they explain differences between Australian fossil faunas and those of other landmasses. Other factors that have contributed include sampling bias, a lack of internal geographic barriers, competition with large terrestrial birds and aspects of island biogeography unique to Australia, such as landmass area and isolation, both temporal and geographic.

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