TheRedTentacle

TheRedTentacle

The hunt for coding numbers, flying satellites and underwater housings.

R Package: Rambo random reductions
Genetic diversity estimation per site or group of sites as standardised allelic richness and standardised number of private alleles determined to the smallest site or group in terms of individuals under a set of randomizations. Those sites or groups of sites with higher standardised A than the global mean are verified by testing the proportion of randomisations retrieving higher values than observed.
File: Rambo.tar.gz

 

# How to use the function
# 1. Set working directory
# ————
# 2. Prepare file # See example by loading the package and the example data file
library(Rambo)
data(Saccorhiza)
# ————
# 3. Define a vector to cluster the populations # Example for 26 populations clustered in 7 groups
clust.vector <- c(1,1,1,2,2,2,2,2,3,3,3,3,3,4,4,4,4,4,4,5,6,6,5,7,7,7,7)
# ————
# 4. Run function
Rambo.mization(data=”filename.txt”,loci=NULL,method=”resamp”,replace=FALSE,resamplenumber.auto=TRUE,resamplenumber.manual=NULL,iteractions=999,alfa=0.05,clustering=FALSE,clustering.vector=clust.vector,savefile=TRUE,filename=“filename”)

R Package: Rambo random reductions

Genetic diversity estimation per site or group of sites as standardised allelic richness and standardised number of private alleles determined to the smallest site or group in terms of individuals under a set of randomizations. Those sites or groups of sites with higher standardised A than the global mean are verified by testing the proportion of randomisations retrieving higher values than observed.

File: Rambo.tar.gz

 

# How to use the function

# 1. Set working directory

# ————

# 2. Prepare file 
# See example by loading the package and the example data file

library(Rambo)

data(Saccorhiza)

# ————

# 3. Define a vector to cluster the populations
# Example for 26 populations clustered in 7 groups

clust.vector <- c(1,1,1,2,2,2,2,2,3,3,3,3,3,4,4,4,4,4,4,5,6,6,5,7,7,7,7)

# ————

# 4. Run function

Rambo.mization(data=”filename.txt”,loci=NULL,method=”resamp”,
replace=FALSE,resamplenumber.auto=TRUE,resamplenumber.manual=NULL,
iteractions=999,alfa=0.05,clustering=FALSE,clustering.vector=clust.vector
,savefile=TRUE,filename=“filename”)

Lagrangian particle simulation for the Portuguese Coast - Version 0.9b

Data from Hybrid Coordinate Ocean Model (HYCOM, Year 2011);

Simulation run for 3 months and followed every 2 hours;

Particles sent per day from Peniche, Cascais and Arrábida, and allowed to travel for 15 days.

Predicting the Arrábida fish assemblages for the last 50 yr revealed that species with tropical affinities have increased in frequency compared to cold-temperate species.
Biogeographic transition zones in marine temperate systems are often hotspots of biodiversity, with high levels of resilience to short-term climate shifts due to naturally occurring cyclic oscillations of oceanographic conditions. However, these environments are likely vulnerable to a steady global warming scenario in which these cyclical conditions could be disrupted. 
In this paper we evaluate how changes in local oceanography affect the structure of rocky reef fish assemblages over a period of 50 yr in Arrábida Marine Park. Using a 12 yr time series of rocky reef fish assemblage structure, we identified the set of oceanographic variables that most influenced assemblage dynamics. 
Winter northward wind stress (Upwelling) and Sea Surface Temperature were the most important drivers of change in assemblage structure. Only warmer years had indicator species with warm-temperate or tropical affinities. 
A model was developed in response to both local-spatial resolution and short-term environmental variation (1993−2011), and to regional spatial resolution and long-term SST (1960−2012). 
Predictive modelling for a novel fish assemblage ‘tropicalization’ index over the last 50 yr revealed that species with tropical affinities have increased in frequency compared to cold-temperate species, coinciding with the trend of increasing mean winter SST. Since the mid-1980s, warm-temperate and tropical species have responded rapidly to more frequent warm winters, suggesting that species distributions are shifting polewards. 
These results support a hypothesis that cold species retreat more slowly than the advance of warm species. 
Continue your readings

Predicting the Arrábida fish assemblages for the last 50 yr revealed that species with tropical affinities have increased in frequency compared to cold-temperate species.

Biogeographic transition zones in marine temperate systems are often hotspots of biodiversity, with high levels of resilience to short-term climate shifts due to naturally occurring cyclic oscillations of oceanographic conditions. However, these environments are likely vulnerable to a steady global warming scenario in which these cyclical conditions could be disrupted. 

In this paper we evaluate how changes in local oceanography affect the structure of rocky reef fish assemblages over a period of 50 yr in Arrábida Marine Park. Using a 12 yr time series of rocky reef fish assemblage structure, we identified the set of oceanographic variables that most influenced assemblage dynamics. 

Winter northward wind stress (Upwelling) and Sea Surface Temperature were the most important drivers of change in assemblage structure. Only warmer years had indicator species with warm-temperate or tropical affinities. 

A model was developed in response to both local-spatial resolution and short-term environmental variation (1993−2011), and to regional spatial resolution and long-term SST (1960−2012). 

Predictive modelling for a novel fish assemblage ‘tropicalization’ index over the last 50 yr revealed that species with tropical affinities have increased in frequency compared to cold-temperate species, coinciding with the trend of increasing mean winter SST. Since the mid-1980s, warm-temperate and tropical species have responded rapidly to more frequent warm winters, suggesting that species distributions are shifting polewards. 

These results support a hypothesis that cold species retreat more slowly than the advance of warm species. 

Continue your readings

When it comes to Posters, Size Matters [!]

We are sailing with 4 posters to the ECSA 54 conference - Coastal systems under change: tuning assessment and management tools.
Our communications will be in the scope of &#8220;Shifts in biodiversity and ecosystem functioning&#8221;
1. Assis, J., Schauls, E., Lucas, A., Aguilar, R., Serrão, E.A. The potential distribution and connectivity of deep kelp forests in the western mediterranean and adjacent atlantic seamounts.
2. Silva, I., Boavida, J., Assis, J., Serrão, E.A.. Predicting future range dynamics under climate change; the case of a structuring coral in its global range.
3. Kelly, R., Assis, J., Schläpfer, N., Serrão, E.A. Invasive species and climate change: an assessment of the global distribution of Undaria pinnatifida for present and future times.
4. Zupan, M., Assis, J., Nicastro, K., Zardi, G., Serrão, E.A. Dispersal or habitat availability: what is limiting the spread of an aggressive marine invader?

We are sailing with 4 posters to the ECSA 54 conference - Coastal systems under change: tuning assessment and management tools.

Our communications will be in the scope of “Shifts in biodiversity and ecosystem functioning”

1. Assis, J., Schauls, E., Lucas, A., Aguilar, R., Serrão, E.A. The potential distribution and connectivity of deep kelp forests in the western mediterranean and adjacent atlantic seamounts.

2. Silva, I., Boavida, J., Assis, J., Serrão, E.A.. Predicting future range dynamics under climate change; the case of a structuring coral in its global range.

3. Kelly, R., Assis, J., Schläpfer, N., Serrão, E.A. Invasive species and climate change: an assessment of the global distribution of Undaria pinnatifida for present and future times.

4. Zupan, M., Assis, J., Nicastro, K., Zardi, G., Serrão, E.A. Dispersal or habitat availability: what is limiting the spread of an aggressive marine invader?