[MARMAM] Reminder: 2017 GoM Oil Spill & Ecosystem Science Conference accepting session proposals through June 24

[suzanne garrett]

 

Don't forget to submit a Scientific Session for the 2017 Gulf of Mexico
Oil Spill and Ecosystem Science Conference. 
 


The 2017 conference theme, “Ecosystem Approaches to Gulf Response and
Restoration,” encourages researchers to consider the application of their
results to practical use.  Looking across a broad range of disciplines,
what have we learned about oil spills and their impacts that can reduce
uncertainty, mitigate ecological, social and health impacts of a future spill,
advance response strategies, and improve how we approach restoration? Using
scientific research will be critical to informing planning, preparedness,
response and recovery for future events, and connecting this to decision
makers in the response and restoration communities will be key. 


The deadline to submit a session proposal is June 24th, 2016.
More information is available on the conference
website. Feel free
to contact us with questions at gulfconfere...@oceanleadership.org.



We are also currently accepting requests for Associated
Events and Workshops to be held Monday, February 6. Space is limited;
however, we will accommodate as many requests as possible. There is no deadline
for workshop requests.








When

February 6 - 9, 2017 



Where

Hyatt Regency New Orleans

601 Loyola Ave, New Orleans, Louisiana 70113, USA

 

~~

Suzanne Garrett

Program Specialist, Gulf of Mexico Research Initiative

Consortium for Ocean Leadership

1201 New York Ave NW | 4th Floor | Washington, D.C.
20005

ph.202.448.1256

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[MARMAM] Phylogenetic data analysis using R

[Oliver Hooker]

"Introduction to phylogenetic analysis with R"

Delivered by Dr. Emmanuel Paradis

http://prstatistics.com/course/introduction-to-phylogenetic-analysis-with-r-phyg/

This course will run from 31st October – 4th November, Millport Field 
Station, Ilse of Cumbrae, Scotland


The main objectives of the course are to teach the theoretical bases of 
phylogenetic analysis, and to give the ability to initiate a 
phylogenetic analysis starting from the files of molecular sequences 
until the interpretation of the results and the graphics. The 
introduction will cover a brief historical background and an overview of 
the different methods of phylogenetic inference. Different kinds of data 
will be considered, but with a special emphasis on DNA sequences. The 
software used will be based on R and several specialized packages 
(particularly ape and phangorn). Other software will be used (e.g., 
MUSCLE or Clustal) called from R. Overall, the course will cover almost 
all aspects of phylogenetic inference from reading/downloading the data 
to plotting the results. This course is intended for PhD and 
postgraduate students, researchers and engineers in evolutionary 
biology, systematics, population genetics, ecology, conservation.


Course content is as follows
Day 1
•	Refresher on R: data structures, data manipulation with the indexing 
system, scripts, using the help system.

•   Introduction to phylogenetic inference.
•	Basics on phylogenetic data (sequences, alignments, trees, networks, 
“splits”) and other data in R.

•   Reading / writing data from files or from internet.
•   Matching data. Manipulating labels. Subsetting data.
•   Main package: ape.
Day 2
•   Plotting and annotating trees.
•	Theory of sequence alignment. Comparing alignments. Graphical 
analyses of alignments.

•   Main packages: ape (with MUSCLE and Clustal).
Day 3
•   Theory and methods of phylogeny reconstruction.
•   Parsimony methods.
•   Evolutionary distances.
•	Distance-based methods: General principles and the main methods (NJ, 
BIONJ, FastME, MVR).
•	Methods for incomplete distances matrices (NJ*, BIONJ*, MVR*). 
Methods for combining several matrices (SDM).

•   Main packages: ape, phangorn.

Day 4
•   Theory of maximum likelihood estimation.
•   Application to phylogeny reconstruction.
•   Substitution models.
•   Tree space and topology estimation.
•   Main packages: ape, phangorn.

Day 5
•   Tree comparison, consensus methods.
•   Topological space and distances.
•   Bootstrap.
•   Bayesian methods.

Please email any inquiries to oliverhoo...@prstatistics.com or visit our 
website www.prstatistics.com


Please feel free to distribute this material anywhere you feel is 
suitable


Upcoming courses - email for details oliverhoo...@prstatistics.com
1.  ADVANCES IN SPATIAL ANALYSIS OF MULTIVARIATE ECOLOGICAL DATA (July)
2.  INTRODUCTION TO BIOINFORMATICS USING LINUX (August)
3.  GENETIC DATA ANALYSIS / EXPLORATION USING R (August)
4.  INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (August)
5.  INTRODUCTION TO PYTHON FOR BIOLOGISTS (October)
6.  LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R (October)
7.	APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS 
(October)

8.  SPATIAL ANALYSIS OF ECOLOGIC AL DATA USING R (November)
9.  ADVANCING IN STATISTICAL MODELLING USING R (December)
10.	MODEL BASED MULTIVARIATE ANALYSIS OF ECOLOGICAL DATA USING R 
(January)

11. ADVACNED PYTHON FOR BIOLOGISTS (February)
12. NETWORK ANALYSIS FOR ECOLOGISTS (March)
13. INTRODUCTION TO GEOMETRIC MORPHOMETRICS USING R (June)

Dates still to be confirmed - email for details 
oliverhoo...@prstatistics.com

•   STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR USING R
•   INTRODUCTION TO R AND STATISTICS FOR BIOLOGISTS
•   BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS

Oliver Hooker
PR statistics

3/1
128 Brunswick Street
Glasgow
G1 1TF

+44 (0) 7966500340

www.prstatistics.com
www.prstatistics.com/organiser/oliver-hooker/
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[MARMAM] Consultation on Species at Risk - proposed Action Plans for the Northern and Southern Resident Killer Whale; and the Blue, Fin, Sei and North Pacific Right Whale

[Thornton, Sheila]

Greetings,

The Minister of Fisheries and Oceans will be posting several federal Species at 
Risk Act Recovery Strategies, Action Plans and Management Plans on the Species 
at Risk Public 
Registry in the 
coming days, including the proposed Action Plan for the Northern and Southern 
Resident Killer Whale (Orcinus orca) in Canada, and the proposed Partial Action 
Plan for Blue, Fin, Sei and North Pacific Right Whales (Balaenoptera musculus, 
B. physalus, B. borealis, and Eubalaena japonica) in Canadian Pacific Waters.

Comments you may have on these proposed recovery documents are requested within 
60 days of each document being posted on the Species at Risk Public Registry. 
You may make your comments through the Public 
Consultation
 page of the Species at Risk Public Registry. I would also encourage you to 
subscribe to the Species at Risk Public Registry email 
newsletter so 
that you receive notifications of public consultations.

Yours sincerely,

Martin Nantel
Acting Regional Manager, Species at Risk Program
Pacific Region
Fisheries and Oceans Canada

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[MARMAM] New publication on toxicants in whale scat - modulation by prey abundance and reproductive factors

[Jessica Lundin]

Hello,
Our manuscript was published in the current issue of Environmental Science
and Technology.  This may of interest to the MARMAM community.  Thanks!

Jessica Lundin


http://pubs.acs.org/doi/abs/10.1021/acs.est.6b00825

Modulation in Persistent Organic Pollutant Concentration and Profile by
Prey Availability and Reproductive Status in Southern Resident Killer Whale
Scat Samples.



Lundin JI, Ylitalo GM, Booth RK, Anulacion B, Hempelmann JA, Parsons KM,
Giles DA, Seely EA, Hanson MB, Emmons CK, Wasser SK.



Environ Sci Technol., 2016, 50 (12), pp 6506–6516

Abstract.  Persistent organic pollutants (POPs), specifically PCBs, PBDEs,
and DDTs, in the marine environment are well documented, however
accumulation and mobilization patterns at the top of the food-web are
poorly understood. This study broadens the understanding of POPs in the
endangered Southern Resident killer whale population by addressing
modulation by prey availability and reproductive status, along with
endocrine disrupting effects. A total of 140 killer whale scat samples
collected from 54 unique whales across a 4 year sampling period (2010–2013)
were analyzed for concentrations of POPs. Toxicant measures were linked to
pod, age, and birth order in genotyped individuals, prey abundance using
open-source test fishery data, and pregnancy status based on hormone
indices from the same sample. Toxicant concentrations were highest and had
the greatest potential for toxicity when prey abundance was the lowest. In
addition, these toxicants were likely from endogenous lipid stores.
Bioaccumulation of POPs increased with age, with the exception of presumed
nulliparous females. The exceptional pattern may be explained by females
experiencing unobserved neonatal loss. Transfer of POPs through
mobilization of endogenous lipid stores during lactation was highest for
first-borns with diminished transfer to subsequent calves. Contrary to
expectation, POP concentrations did not demonstrate an associated
disruption of thyroid hormone, although this association may have been
masked by impacts of prey abundance on thyroid hormone concentrations. The
noninvasive method for measuring POP concentrations in killer whales
through scat employed in this study may improve toxicant monitoring in the
marine environment and promote conservation efforts.
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[MARMAM] PICES sessions in San Diego

[Elliott Hazen]

Hi all,

The 25th anniversary of PICES is in San Diego, CA from Nov. 1 - 14. There are 
two relevant sessions entitled "Factors that make or break trophic linkages" 
with ecologists, oceanographers, and social scientists and "Understanding our 
Changing Oceans through Species Distributions and Habitat Models based on 
Remotely Sensed Data." You can submit an abstract here if interested, and the 
due date is July 1st - 
http://meetings.pices.int/meetings/annual/2016/pices/submissions

The session descriptions are below:

Mechanistic linkages from physics to phytoplankton to zooplankton to fish 
remain central to understanding climate forcing on marine ecosystems. Thus, it 
will be useful to understand how ecosystem linkages and species distribution 
are influenced by ocean features and how these linkages translate through the 
food web. Specifically, what information can be gained from moving beyond a 
single linkage (e.g. phytoplankton to zooplankton) towards a comparison across 
trophic levels in three very different North Pacific ecosystems. Examples of 
such factors may include but are not limited to broad scale anomalies (e.g. the 
blob, ENSO events, Kuroshio / Oyashio dynamics), temporal mismatches among 
physical processes, prey, and predators (match / mismatch hypothesis), and 
population fluctuations (e.g. lipid poor vs. lipid rich zooplankton). We have 
suggested (but are not limited to) three study areas, the California Current, 
the Kuroshio Current, and the Bering Sea to examine linkages from physics to 
phytoplankton, phytoplankton to zooplankton, zooplankton to fish, birds and 
mammals, and fish to birds and mammals. By looking at multiple ecosystems and 
trends and anomalies across multiple trophic linkages, we can better understand 
how climate variability and anthropogenic forcing may cascade through these 
marine ecosystems. We propose a topic session that will involve participation 
from multiple PICES committees and will focus on physical forcing and trophic 
linkages from physics to top predators. Specifically, we request presentations 
on topics that (a) examine how changes in physical oceanography lead to long 
term trends or anomalous responses in primary production, zooplankton, fish, 
and top predators, (b) examine how trophic relationships may respond to 
physical forcing and changes in species abundance and spatial distribution, and 
(c) test for threshold responses (non-linearity) across trophic levels to 
changes in physical oceanography and the population dynamics of other species 
(competitors, prey, and predators).

Determining marine animal distributions directly through at-sea observations or 
tracking is costly and logistically challenging. Moreover, even with limitless 
time and resources, information is limited because many species disperse over 
long distances including trans-hemispheric migrants. Species Distribution 
Models (SDMs) provide a tool to estimate present distributions and to project 
into the future (assuming species-environment relationships remain strong), but 
these models require substantial environmental data to accurately predict 
distribution and change. Increasingly, SDM approaches rely on remotely-sensed 
satellite data as indices of environmental conditions, particularly as proxies 
for primary and possibly secondary productivity. Satellite datasets are 
inexpensive to use, widely served, well-documented (i.e., scientifically 
defensible), and globally synoptic, allowing for easy spatio-temporal 
comparisons. However, satellite-borne sensors measure characteristics of the 
ocean at the surface while marine organisms respond to spatial and temporal 
features of the ocean at depth, which may require more complex approaches. In 
this session, we will investigate the opportunities and challenges of using 
satellite-based habitat models and ways we can advance SDMs for a better 
understanding our changing oceans and for improving management. In particular, 
we solicit papers exploring the benefits and tradeoffs of using satellite-borne 
data to detect mechanisms of distributional and range shifts. This session will 
provide the PICES community and the FUTURE program with a better sense of the 
quality of fisheries, seabird, and marine mammal SDM under development in 
relation to climate change in the North Pacific.

Sincerely,
Elliott Hazen, PhD
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