Compositional Analysis in Behavioural and Evolutionary Ecology

Pierotti, Michele E. R.; Martín‐Fernández, Josep Antoni

doi:10.1002/9781119976462.ch16

Cited by 6 publications

(5 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Except for somatic indices, all other data were expressed as percentages or proportions. Compositional data are very common across ecology, behaviour and evolution ( Pierotti and Martín-Fernaández, 2011 ; Greenacre, 2021 ), but poses a challenge to common statistical methods. In this case, we used a PCA for compositional data ( Aitchison, 1983 ) in the R package compositions ( van den Boogaart and Tolosana-Delgado, 2008 ).…”

Section: Methodsmentioning

confidence: 99%

Multiple morphophysiological responses of a tropical frog to urbanization conform to the pace-of-life syndrome

Franco-Belussi,

de Oliveira Júnior,

Goldberg

et al. 2024

Conservation Physiology

View full text Add to dashboard Cite

The Pace-of-Life syndrome proposes that behavioural, physiological and immune characteristics vary along a slow-fast gradient. Urbanization poses several physiological challenges to organisms. However, little is known about how the health status of frogs is affected by urbanization in the Tropics, which have a faster and more recent urbanization than the northern hemisphere. Here, we analysed a suite of physiological variables that reflect whole organism health, reproduction, metabolic and circulatory physiology and leukocyte responses in Leptodactylus podicipinus. Specifically, we tested how leukocyte profile, erythrocyte morphometrics and germ cell density, as well as somatic indices and erythrocyte nuclear abnormalities differ throughout the adult life span between urban and rural populations. We used Phenotypic Trajectory Analysis to test the effect of age and site on each of the multivariate data sets; and a Generalised Linear Model to test the effect of site and age on nuclear abnormalities. Somatic indices, erythrocyte nuclear abnormalities, erythrocyte morphometrics and leukocyte profile differed between populations, but less so for germ cell density. We found a large effect of site on nuclear abnormalities, with urban frogs having twice as many abnormalities as rural frogs. Our results suggest that urban frogs have a faster pace of life, but the response of phenotypic compartments is not fully concerted.

show abstract

Section: Methodsmentioning

confidence: 99%

Multiple morphophysiological responses of a tropical frog to urbanization conform to the pace-of-life syndrome

Franco-Belussi,

de Oliveira Júnior,

Goldberg

et al. 2024

Conservation Physiology

View full text Add to dashboard Cite

show abstract

“…Notably, CoDA methods overcome constant sum constraints that are characteristic of many analyses ( i.e., the assumption that all samples sum to a constant, such as 1 or 100%), enabling us to analyze DEMs of different total areas, in which compositional components could vary independently from one another ( Aitchison, 2003a ). Whereas the use of traditional statistical techniques on compositional data yields multicollinearity and unreliable estimates ( Kucera & Malmgren, 1998 ; Aitchison, 2003b ; Graham, 2003 ; Dormann et al, 2013 ; Douma & Weedon, 2019 ), advancements in CoDA methods provide valuable and broadly applicable techniques to assess compositional data, which continue to gain recognition across disciplines ( Reyment, 1989 ; Baker, 2008 ; Campbell et al, 2009 ; Pierotti & Martín-Ferńandez, 2011 ; del Pozo Cruz et al, 2020 ). We performed all CoDA analyses in R, version 3.6.1 ( R Core Team, 2013 ), using the compositions , robCompositions , and zCompositions packages ( Palarea-Albaladejo & Martín-Fernández, 2020 ; Templ et al, 2020 ; van den Boogaart, Tolosana-delgado & Bren, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Dead but not forgotten: complexity of Acropora palmata colonies increases with greater composition of dead coral

Engleman,

Cox,

Brooke

2023

PeerJ

View full text Add to dashboard Cite

Coral reefs are highly biodiverse ecosystems that have declined due to natural and anthropogenic stressors. Researchers often attribute reef ecological processes to corals’ complex structure, but effective conservation requires disentangling the contributions of coral versus reef structures. Many studies assessing the relationships between reef structure and ecological dynamics commonly use live coral as a proxy for reef complexity, disregarding the contribution of dead coral skeletons to reef habitat provision or other biogeochemical reef dynamics. This study aimed to assess the contribution of dead coral to reef complexity by examining structural variations in live and dead Acropora palmata colonies. We used photogrammetry to reconstruct digital elevation models (DEMs) and orthomosaics of the benthic region immediately surrounding 10 A. palmata colonies. These reconstructions were used to quantify structural metrics, including surface rugosity, fractal dimension, slope, planform curvature, and profile curvature, as a function of benthic composition (i.e., live A. palmata, dead A. palmata, or non-A. palmata substrate). The results revealed that dead coral maintained more varied profile curvatures and higher fractal dimensions than live or non-coral substrate. Conversely, A. palmata colonies with a higher proportion of live coral displayed more uniform structure, with lower fractal dimensions and less variability in profile curvature measures. Other metrics showed no significant difference among substrate types. These findings provide novel insights into the structural differences between live and dead coral, and an alternative perspective on the mechanisms driving the observed structural complexity on reefs. Overall, our results highlight the overlooked potential contributions of dead coral to reef habitat provision, ecological processes, and other biogeochemical reef dynamics, and could have important implications for coral reef conservation.

show abstract

“…Ever since John Aitchison provided solutions to spurious statistics using compositional data [46], the transformation from proportions to log-ratios has been widely adopted in soil [38,47,48] and life science studies [49,50]. The simplex constituted with proportions of carbon and nitrogen; as well as the non-overlapping mineral composition of sand, silt, and clay; was transformed into isometric log-ratios ( ilr ) [51] to generate balances of components.…”

Section: Methodsmentioning

confidence: 99%

Using a soil bacterial species balance index to estimate potato crop productivity

2019

View full text Add to dashboard Cite

The development of ‘molecular-omic’ tools and computing analysis platforms have greatly enhanced our ability to assess the impacts of agricultural practices and crop management protocols on soil microbial diversity. However, biotic factors are rarely factored into agricultural management models. Today it is possible to identify specific microbiomes and define biotic components that contribute to soil quality. We assessed the bacterial diversity of soils in 51 potato production plots. We describe a strategy for identifying a potato-crop-productivity bacterial species balance index based on amplicon sequence variants. We observed a significant impact of soil texture balances on potato yields; however, the Shannon and Chao1 richness indices and Pielou’s evenness index poorly correlated with these yields. Nonetheless, we were able to estimate the portion of the total bacterial microbiome related to potato yield using an integrated species balances index derived from the elements of the bacterial microbiome that positively or negatively correlate with residual potato yields. This innovative strategy based on a microbiome selection procedure greatly enhances our ability to interpret the impact of agricultural practices and cropping system management choices on microbial diversity and potato yield. This strategy provides an additional tool that will aid growers and the broader agricultural sector in their decision-making processes concerning the soil quality and crop productivity.

show abstract

Compositional Analysis in Behavioural and Evolutionary Ecology

Cited by 6 publications

References 48 publications

Multiple morphophysiological responses of a tropical frog to urbanization conform to the pace-of-life syndrome

Multiple morphophysiological responses of a tropical frog to urbanization conform to the pace-of-life syndrome

Dead but not forgotten: complexity of Acropora palmata colonies increases with greater composition of dead coral

Using a soil bacterial species balance index to estimate potato crop productivity

Contact Info

Product

Resources

About