Persistent fire effect on forest dynamics and species composition of an old-growth tropical forest

Aim of the study: To assess structure, recruitment and mortality rates of tree species over almost three decades, 14 years before and 15 years after a forest fire. Material and methods: All trees ≥ 5 cm in DBH were identified and measured in 12 permanent plots (50 m x 50 m), in 1983, 1987, 1989, 1995, 2008, and 2012 of a dense ombrophilous forest in Eastern Amazon, Brazil. The analyses were carried out including all sampled species and their ecological groups: shade-tolerant, light-demanding, and pioneer species. Treatments were compared through a Linear Mixed Effect Model. Main results: The 15-year post-fire period is not enough for the old-growth tropical forest to recover its pre-fire conditions of recruitment and mortality rates. The post-fire recruitment and mortality rates increased, mainly the recruitment of pioneer species (p-value < 0.05). Research highlights: In a period of 15 years after the occurrence of a surface fire, the old-growth tropical forest still has high recruitment rates of shade-tolerant and light-demanding species and high incidence of pioneer species, confirming the persistent fire effects on forest dynamics and species composition in this ecosystem.

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Bryophyte Conservation in Managed Boreal Landscapes: Fourteen-Year Impacts of Partial Cuts on Epixylic Bryophytes

Frontiers in Forests and Global Change ◽

10.3389/ffgc.2021.674887 ◽

2021 ◽

Vol 4 ◽

Author(s):

Jeffrey Opoku-Nyame ◽

Alain Leduc ◽

Nicole J. Fenton

Keyword(s):

Species Composition ◽

Coarse Woody Debris ◽

Black Spruce ◽

Woody Debris ◽

Permanent Plots ◽

Old Growth ◽

Clear Cut ◽

Old Growth Forest ◽

Old Growth Forests ◽

Over Time

Clear cut harvest simplifies and eliminates old growth forest structure, negatively impacting biodiversity. Partial cut harvest has been hypothesized (1) to have less impact on biodiversity than clear cut harvest, and (2) to encourage old growth forest structures. Long-term studies are required to test this hypothesis as most studies are conducted soon after harvest. Using epixylic bryophytes as indicators, this study addresses this knowledge gap. Fourteen years after harvest, we examined changes in epixylic bryophyte community composition richness and traits, and their microhabitats (coarse woody debris characteristics and microclimate) along an unharvested, partial cuts and clear cuts harvest treatment in 30 permanent plots established in the boreal black spruce (Picea mariana) forests of northwestern Quebec, Canada. Our results were compared to those of an initial post-harvest study (year 5) and to a chronosequence of old growth forests to examine species changes over time and the similarity of bryophyte communities in partial cut and old growth forests. Coarse woody debris (CWD) volume by decay class varied among harvest treatments with partial cuts and clear cuts recording lower volumes of early decay CWD. The epixylic community was richer in partial cuts than in mature unharvested forests and clear cuts. In addition, species richness and overall abundance doubled in partial and clear cuts between years 5 and 14. Species composition also differed among treatments between years 5 and 14. Furthermore, conditions in partial cut stands supported small, drought sensitive, and old growth confined species that are threatened by conditions in clear cut stands. Lastly, over time, species composition in partial cuts became more similar to old growth forests. Partial cuts reduced harvest impacts by continuing to provide favorable microhabitat conditions that support epixylic bryophytes. Also, partial cut harvest has the potential to encourage old growth species assemblages, which has been a major concern for biodiversity conservation in managed forest landscapes. Our findings support the promotion of partial cut harvest as an effective strategy to achieve species and habitat conservation goals.

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After trees die: quantities and determinants of necromass across Amazonia

Biogeosciences ◽

10.5194/bg-6-1615-2009 ◽

2009 ◽

Vol 6 (8) ◽

pp. 1615-1626 ◽

Cited By ~ 38

Author(s):

K.-J. Chao ◽

O. L. Phillips ◽

T. R. Baker ◽

J. Peacock ◽

G. Lopez-Gonzalez ◽

...

Keyword(s):

Wood Density ◽

Forest Structure ◽

Forest Dynamics ◽

Amazon Basin ◽

Mortality Rates ◽

Permanent Plots ◽

Mortality Data ◽

Terra Firma ◽

Amazonian Forests ◽

Stem Mortality

Abstract. The Amazon basin, one of the most substantial biomass carbon pools on earth, is characterised by strong macroecological gradients in biomass, mortality rates, and wood density from west to east. These gradients could affect necromass stocks, but this has not yet been tested. This study aims to assess the stocks and determinants of necromass across Amazonian forests. Field-based and literature data were used to find relationships between necromass and possible determinants. Furthermore, a simple model was applied to estimate and extrapolate necromass stocks across terra firma Amazonian forests. In eight northwestern and three northeastern Amazonian permanent plots, volumes of coarse woody debris (≥10 cm diameter) were measured in the field and the density of each decay class was estimated. Forest structure and historical mortality data were used to determine the factors controlling necromass. Necromass is greater in forests with low stem mortality rates (northeast) rather than in forests with high stem mortality rates (northwest) (58.5±10.6 and 27.3±3.2 Mg ha−1, respectively). Using all published necromass values, we find that necromass across terra firma forests in Amazonia is positively related to both forest dynamics (mortality mass inputs and a surrogate for decomposition rate (average wood density of living trees)) and forest structure (biomass), but is better explained by forest dynamics. We propose an improved method to estimate necromass for plots where necromass has not been measured. The estimates, together with other actual measurements of necromass, were scaled-up to project a total Amazonian necromass of 9.6±1.0 Pg C. The ratio of necromass (on average weighted by forest region) to coarse aboveground biomass is 0.127. Overall, we find (1) a strong spatial trend in necromass in parallel with other macroecological gradients and (2) that necromass is a substantial component of the carbon pool in the Amazon.

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The Role of Canopy Cover Dynamics over a Decade of Changes in the Understory of an Atlantic Beech-Oak Forest

Forests ◽

10.3390/f12070938 ◽

2021 ◽

Vol 12 (7) ◽

pp. 938

Author(s):

Mercedes Valerio ◽

Ricardo Ibáñez ◽

Antonio Gazol

Keyword(s):

Species Composition ◽

Temperate Forests ◽

Light Availability ◽

Structural Complexity ◽

Understory Vegetation ◽

Permanent Plots ◽

Oak Forest ◽

Gap Dynamics ◽

Gap Formation ◽

Old Growth

The understory of temperate forests harbour most of the plant species diversity present in these ecosystems. The maintenance of this diversity is strongly dependent on canopy gap formation, a disturbance naturally happening in non-managed forests, which promotes spatiotemporal heterogeneity in understory conditions. This, in turn, favours regeneration dynamics, functioning and structural complexity by allowing changes in light, moisture and nutrient availability. Our aim is to study how gap dynamics influence the stability of understory plant communities over a decade, particularly in their structure and function. The study was carried out in 102 permanent plots (sampled in 2006 and revisited in 2016) distributed throughout a 132 ha basin located in a non-managed temperate beech-oak forest (Bertiz Natural Park, Spain). We related changes in the taxonomical and functional composition and diversity of the understory vegetation to changes in canopy coverage. We found that gap dynamics influenced the species composition and richness of the understory through changes in light availability and leaf litter cover. Species with different strategies related to shade tolerance and dispersion established in the understory following the temporal evolution of gaps. However, changes in understory species composition in response to canopy dynamics occur at a slow speed in old-growth temperate forests, needing more than a decade to really be significant. The presence of gaps persisting more than ten years is essential for maintaining the heterogeneity and stability of understory vegetation in old-growth temperate forests.

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Identifying climatic drivers of tropical forest dynamics

Biogeosciences ◽

10.5194/bg-12-5583-2015 ◽

2015 ◽

Vol 12 (19) ◽

pp. 5583-5596 ◽

Cited By ~ 12

Author(s):

M. Aubry-Kientz ◽

V. Rossi ◽

F. Wagner ◽

B. Hérault

Keyword(s):

Tropical Forest ◽

Forest Dynamics ◽

Water Saturation ◽

Selection Procedure ◽

Mortality Rates ◽

Climate Impacts ◽

Climatic Variables ◽

Small Current ◽

Climatic Drivers ◽

Tropical Forest Dynamics

Abstract. In the context of climate change, identifying and then predicting the impacts of climatic drivers on tropical forest dynamics is becoming a matter of urgency. To look at these climate impacts, we used a coupled model of tropical tree growth and mortality, calibrated with forest dynamic data from the 20-year study site of Paracou, French Guiana, in order to introduce and test a set of climatic variables. Three major climatic drivers were identified through the variable selection procedure: drought, water saturation and temperature. Drought decreased annual growth and mortality rates, high precipitation increased mortality rates and high temperature decreased growth. Interactions between key functional traits, stature and climatic variables were investigated, showing best resistance to drought for trees with high wood density and for trees with small current diameters. Our results highlighted strong long-term impacts of climate variables on tropical forest dynamics, suggesting potential deep impacts of climate changes during the next century.

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Identifying climatic drivers of tropical forest dynamics

Biogeosciences Discussions ◽

10.5194/bgd-12-3145-2015 ◽

2015 ◽

Vol 12 (3) ◽

pp. 3145-3176 ◽

Cited By ~ 2

Author(s):

M. Aubry-Kientz ◽

V. Rossi ◽

F. Wagner ◽

B. Hérault

Keyword(s):

Tropical Forest ◽

Forest Dynamics ◽

Climate Changes ◽

Water Saturation ◽

Selection Procedure ◽

Mortality Rates ◽

Climatic Variables ◽

Small Current ◽

Climatic Drivers ◽

Tropical Forest Dynamics

Abstract. In the context of climate changes, identifying and then predicting the impacts of climatic drivers on tropical forest dynamics is becoming a matter of urgency. We used a coupled model of tropical tree growth and mortality, calibrated with forest dynamic data from the 20 year study site of Paracou, French Guiana, in order to introduce and test a set of climatic variables. Three major climatic drivers were identified through the variable selection procedure: drought, water saturation and temperature. Drought decreased annual growth and mortality rates, high precipitation increased mortality rates and high temperature decreased growth. Interactions between key functional traits, stature and climatic variables were investigated, showing best resistance to drought for trees with high wood density and for trees with small current diameters. Our results highlighted strong long-term impacts of climate variables on tropical forest dynamics, suggesting potential deep impacts of climate changes during the next century.

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Carabidae of Barnaul city parks: ecological characteristics and species composition

Ukrainian Journal of Ecology ◽

10.15421/2018_353 ◽

2018 ◽

Vol 8 (2) ◽

pp. 348-353

Author(s):

E. A. Kuchina ◽

N. D. Ovcharenko ◽

L. D. Vasileva

Keyword(s):

Species Composition ◽

Diversity Index ◽

Similarity Index ◽

Life Forms ◽

Ground Beetles ◽

Forest Steppe ◽

Ecological Groups ◽

Dominant Group ◽

Species Diversity Index ◽

Steppe Species

<p>Anthropogenic impact on the population of ground beetles leads to a change in their numbers, structure of dominance, density, species composition, spectrum of life forms. This makes the beetles Carabidae a convenient and informative bioindicator of the ecological state of biocenoses. The material for this work was the Carabidae collections conducted in June-August 2016-2017 in the park zone of different regions of Barnaul, differing in location, area, hydrological regime, vegetation cover, purpose and anthropogenic load. When processing the material, the quantitative, species and generic composition of the carabidae was determined, calculations were made for such indicators as the Berger-Parker dominance index, the Shannon species diversity index (Hs), and the Jacquard species similarity index. The fauna (Coleoptera, Carabidae) of the park zone of Barnaul is represented by 55 species belonging to 20 genera. The dominant group is represented by species belonging to steppe, forest and polyzonal groups. Forest-steppe species of ground beetles as dominants have not been identified in any of the investigated territories. The greatest variety of ecological groups was noted on the territory of the Yubileyny рark, which is explained by the presence of zones with various microclimatic conditions, the presence of a birch grove that flows through the park with the Pivovarka River, and a wide log in the park. Registered species belong to eight groups of life forms belonging to two classes - zoophagous and myxophytophagous. On the numerical and species abundance, zoophages predominate. The spectrum of life forms corresponds to the zonal spectrum characteristic of the forest-steppe zone.</p><p> </p>

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MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits

Genome Biology ◽

10.1186/s13059-021-02416-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Daniel E. Runcie ◽

Jiayi Qu ◽

Hao Cheng ◽

Lorin Crawford

Keyword(s):

Genomic Prediction ◽

Large Scale ◽

Mixed Model ◽

Human Genetics ◽

Linear Mixed Effect Model ◽

Mixed Effect ◽

Statistical Framework ◽

Effect Model ◽

Plant Data ◽

Genetic Value

AbstractLarge-scale phenotype data can enhance the power of genomic prediction in plant and animal breeding, as well as human genetics. However, the statistical foundation of multi-trait genomic prediction is based on the multivariate linear mixed effect model, a tool notorious for its fragility when applied to more than a handful of traits. We present , a statistical framework and associated software package for mixed model analyses of a virtually unlimited number of traits. Using three examples with real plant data, we show that can leverage thousands of traits at once to significantly improve genetic value prediction accuracy.

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Sept8/SEPTIN8 involvement in cellular structure and kidney damage is identified by genetic mapping and a novel human tubule hypoxic model

Scientific Reports ◽

10.1038/s41598-021-81550-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Gregory R. Keele ◽

Jeremy W. Prokop ◽

Hong He ◽

Katie Holl ◽

John Littrell ◽

...

Keyword(s):

Complex Traits ◽

Genetic Model ◽

Association Studies ◽

Model Systems ◽

Linear Mixed Effect Model ◽

Genome Wide Association Studies ◽

Tubulointerstitial Injury ◽

Heritable Variation ◽

Mixed Effect

AbstractChronic kidney disease (CKD), which can ultimately progress to kidney failure, is influenced by genetics and the environment. Genes identified in human genome wide association studies (GWAS) explain only a small proportion of the heritable variation and lack functional validation, indicating the need for additional model systems. Outbred heterogeneous stock (HS) rats have been used for genetic fine-mapping of complex traits, but have not previously been used for CKD traits. We performed GWAS for urinary protein excretion (UPE) and CKD related serum biochemistries in 245 male HS rats. Quantitative trait loci (QTL) were identified using a linear mixed effect model that tested for association with imputed genotypes. Candidate genes were identified using bioinformatics tools and targeted RNAseq followed by testing in a novel in vitro model of human tubule, hypoxia-induced damage. We identified two QTL for UPE and five for serum biochemistries. Protein modeling identified a missense variant within Septin 8 (Sept8) as a candidate for UPE. Sept8/SEPTIN8 expression increased in HS rats with elevated UPE and tubulointerstitial injury and in the in vitro hypoxia model. SEPTIN8 is detected within proximal tubule cells in human kidney samples and localizes with acetyl-alpha tubulin in the culture system. After hypoxia, SEPTIN8 staining becomes diffuse and appears to relocalize with actin. These data suggest a role of SEPTIN8 in cellular organization and structure in response to environmental stress. This study demonstrates that integration of a rat genetic model with an environmentally induced tubule damage system identifies Sept8/SEPTIN8 and informs novel aspects of the complex gene by environmental interactions contributing to CKD risk.

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Limited not lazy: a quasi-experimental secondary analysis of evidence quality evaluations by those who hold implausible beliefs

Cognitive Research Principles and Implications ◽

10.1186/s41235-020-00264-z ◽

2020 ◽

Vol 5 (1) ◽

Author(s):

Kristy A. Martire ◽

Bethany Growns ◽

Agnes S. Bali ◽

Bronte Montgomery-Farrer ◽

Stephanie Summersby ◽

...

Keyword(s):

Secondary Analysis ◽

Past Research ◽

Linear Mixed Effect Model ◽

High Quality ◽

Mixed Effect ◽

High Quality Evidence ◽

Effect Model ◽

Evidence Quality ◽

Quasi Experimental ◽

Quality Evidence

AbstractPast research suggests that an uncritical or ‘lazy’ style of evaluating evidence may play a role in the development and maintenance of implausible beliefs. We examine this possibility by using a quasi-experimental design to compare how low- and high-quality evidence is evaluated by those who do and do not endorse implausible claims. Seven studies conducted during 2019–2020 provided the data for this analysis (N = 746). Each of the seven primary studies presented participants with high- and/or low-quality evidence and measured implausible claim endorsement and evaluations of evidence persuasiveness (via credibility, value, and/or weight). A linear mixed-effect model was used to predict persuasiveness from the interaction between implausible claim endorsement and evidence quality. Our results showed that endorsers were significantly more persuaded by the evidence than non-endorsers, but both groups were significantly more persuaded by high-quality than low-quality evidence. The interaction between endorsement and evidence quality was not significant. These results suggest that the formation and maintenance of implausible beliefs by endorsers may result from less critical evidence evaluations rather than a failure to analyse. This is consistent with a limited rather than a lazy approach and suggests that interventions to develop analytical skill may be useful for minimising the effects of implausible claims.

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Associations between the Bovine Myostatin Gene and Milk Fatty Acid Composition in New Zealand Holstein-Friesian × Jersey-Cross Cows

Animals ◽

10.3390/ani10091447 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1447

Author(s):

Ishaku L. Haruna ◽

Yunhai Li ◽

Ugonna J. Ekegbu ◽

Hamed Amirpour-Najafabadi ◽

Huitong Zhou ◽

...

Keyword(s):

Fatty Acid ◽

New Zealand ◽

Nucleotide Sequence ◽

Milk Fat ◽

Linear Mixed Effect Model ◽

Polymorphism Analysis ◽

Mixed Effect ◽

Myostatin Gene ◽

Holstein Friesian ◽

Nucleotide Sequence Variation

The myostatin gene (MSTN), which encodes the protein myostatin, is pleiotropic, and its expression has been associated with both increased and decreased adipogenesis and increased skeletal muscle mass in animals. In this study, the polymerase chain reaction, coupled with single strand conformation polymorphism analysis, was utilized to reveal nucleotide sequence variation in bovine MSTN in 410 New Zealand (NZ) Holstein-Friesian × Jersey (HF × J)-cross cows. These cows ranged from 3 to 9 years of age and over the time studied, produced an average 22.53 ± 2.18 L of milk per day, with an average milk fat content of 4.94 ± 0.17% and average milk protein content of 4.03 ± 0.10%. Analysis of a 406-bp amplicon from the intron 1 region, revealed five nucleotide sequence variants (A–E) that contained seven nucleotide substitutions. Using general linear mixed-effect model analyses the AD genotype was associated with reduced C10:0, C12:0, and C12:1 levels when compared to levels in cows with the AA genotype. These associations in NZ HF × J cross cows are novel, and they suggest that this variation in bovine MSTN could be explored for increasing the amount of milk unsaturated fatty acid and decreasing the amount of saturated fatty acid.

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