[MARMAM] New publication: Group feeding recorded in leopard seals

[James Robbins]

Dear Colleagues,
On behalf of my co-authors, I am pleased to announce that the following
article has been published in *Polar Biology*:

Robbins JR, Poncet D, Evans AR, Hocking, DP. (2019). A rare observation of
group prey processing in wild leopard seals (*Hydrurga leptonyx*).
https://doi.org/10.1007/s00300-019-02542-z

Abstract:
Cooperative feeding is often observed among predators with strong social
bonds; however, it is unexpected in solitary predators. During 2016,
several mass predation events were witnessed in St Andrews Bay and Right
Whale Bay, South Georgia, where up to 36 leopard seals (*Hydrurga leptonyx*)
were seen feeding together at king penguin (*Aptenodytes patagonicus*)
colonies. Three post-mortem prey-processing events were observed where two
leopard seals actively fed on the same carcass in an unusual display of
tolerance for a species where anti-social behaviour is the norm. The seals
were observed repeatedly tearing adult king penguins between themselves,
while floating alongside each other at the surface of the water. This is
the first record of co-feeding in this difficult-to-study species; however,
it is expected that the behaviour is rare within the population. We propose
that the high density of predators combined with the readily available
prey, makes it costlier to defend a kill than it is to tolerate
kleptoparasitism. It is unclear whether this behaviour shows cooperative
feeding, which would likely enable more efficient prey processing: by
holding the prey in their jaws, each seal provides an anchor on the prey
that others can pull against to stretch and tear it.

The article can be accessed with the following link, but feel free to
contact me (jamesrichardrobb...@googlemail.com) for a PDF.
https://link.springer.com/article/10.1007/s00300-019-02542-z

Best wishes,
James Robbins
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[MARMAM] New paper on killer whale genomics

[Andy Foote]

Dear colleagues,

We are pleased to announce the publication of our new paper analysing a
global dataset of killer whales in the current issue of Molecular Ecology (
https://doi.org/10./mec.15099) and is accompanied by a perspective
piece focusing on a key finding of archaic 'ghost' ancestry in the
Antarctic types (https://doi.org/10./mec.15141).

To help non-geneticists follow the methods used and the interpretation of
results in this study, I've posted a walk through of the results (
https://www.youtube.com/watch?v=KtfVBVFNDMM&t=11s). I will try and upload a
more polished and scripted version soon. And I hope to upload more overview
videos to this Footenotes channel and a website (footenotes.org) under
construction.

The abstract of the paper is pasted below.

- Andy Foote and coauthors



Killer whale genomes reveal a complex history of recurrent admixture and
vicariance

Andrew D. Foote,  Michael D. Martin,  Marie Louis,  George Pacheco,  Kelly
M. Robertson,  Mikkel‐Holger S. Sinding,  Ana R. Amaral,  Robin W. Baird,
 Charles Scott Baker,  Lisa Ballance,  Jay Barlow,  Andrew Brownlow,  Tim
Collins,  Rochelle Constantine,  Willy Dabin,  Luciano Dalla Rosa,
 Nicholas J. Davison,  John W. Durban,  Ruth Esteban,  Steven H. Ferguson,
 Tim Gerrodette,  Christophe Guinet,  M. Bradley Hanson, Wayne Hoggard,
 Cory J. D. Matthews,  Filipa I. P. Samarra,  Renaud de Stephanis,  Sara B.
Tavares,  Paul Tixier,  John A. Totterdell,  Paul Wade,  Laurent Excoffier,
 M. Thomas P. Gilbert,  Jochen B. W. Wolf &  Phillip A. Morin

Reconstruction of the demographic and evolutionary history of populations
assuming a consensus tree‐like relationship can mask more complex
scenarios, which are prevalent in nature. An emerging genomic toolset,
which has been most comprehensively harnessed in the reconstruction of
human evolutionary history, enables molecular ecologists to elucidate
complex population histories. Killer whales have limited extrinsic barriers
to dispersal and have radiated globally, and are therefore a good candidate
model for the application of such tools. Here, we analyse a global data set
of killer whale genomes in a rare attempt to elucidate global population
structure in a nonhuman species. We identify a pattern of genetic
homogenisation at lower latitudes and the greatest differentiation at high
latitudes, even between currently sympatric lineages. The processes
underlying the major axis of structure include high drift at the edge of
species' range, likely associated with founder effects and allelic surfing
during postglacial range expansion. Divergence between Antarctic and
non‐Antarctic lineages is further driven by ancestry segments with up to
four‐fold older coalescence time than the genome‐wide average; relicts of a
previous vicariance during an earlier glacial cycle. Our study further
underpins that episodic gene flow is ubiquitous in natural populations, and
can occur across great distances and after substantial periods of isolation
between populations. Thus, understanding the evolutionary history of a
species requires comprehensive geographic sampling and genome‐wide data to
sample the variation in ancestry within individuals.
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[MARMAM] New publication: hypopigmentation in fin whale

[Severine Methion]

Dear MARMAM colleagues,

We are pleased to announce our new publication:

Methion S, Diaz Lopez B (2019). First record of atypical pigmentation pattern 
in fin whale Balaenoptera physalus in the Atlantic Ocean. Diseases of Aquatic 
Organisms 135:121-125. DOI: 10.3354/dao03385 

Abstract
Atypical pigmentation, which is rarely observed in the wild, may influence 
social interactions between animals and can be detrimental for survival. 
Hypopigmentation, which is the lack of pigment in a part or on the entire body, 
is a type of atypical pigmentation pattern that can be either acquired (e.g. 
vitiligo) or congenital resulting from the inheritance of mutations in 
pigment-related genes (e.g. albinism, leucism and piebaldism). This study 
documents atypical pigmentation in a fin whale (Balaenoptera physalus) along 
the northwestern coast of the Iberian Peninsula (Atlantic Ocean). Photographic 
and video data collected between 2016 and 2017 on 30 individual fin whales were 
examined. One fully-grown fin whale exhibited hypopigmentation. Several white 
patches of different shapes and sizes were present across the body of the fin 
whale including on the head, body, dorsal fin, flippers, and flukes. The 
position, shape, and lack of inflammation of the white patches on the whale 
observed, along with its body length and condition might indicate that the 
depigmentation pattern is due to vitiligo. To our knowledge, this is the first 
case of atypical pigmentation pattern in fin whales described with photographs 
and video records. As these observations are rare, especially in highly 
migratory, long-lived, marine mammal species, this study provides valuable 
information to better understand the occurrence of this phenomenon. Further 
studies are needed to determine the ecological and physiological implications 
of abnormal colourations, which might have a significant influence on the 
animal´s survival.

The article can be found at the following link: 
https://www.int-res.com/abstracts/dao/v135/n2/p121-125/

Feel free to contact me to request a pdf or for any question regarding our work 
at: sever...@thebdri.com

Best regards,

Severine Methion, MSc
PhD candidate, Université de Bordeaux
Bottlenose Dolphin Research Institute BDRI
Av. Beiramar 192, 36980, O Grove, Pontevedra, Spain
www.thebdri.com

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[MARMAM] R Package design and development and reproducible data science for biologists - FREE ACCOMMODATION

[Oliver Hooker]

COURSE ON - R Package design and development and reproducible data
science for biologists (RPKG01) with free accommodation.

PR statistics now has a new accommodation option implemented allowing
a limited amount of places with free accommodation. The next 5 people
to register for this course will receive free accommodation if they
require it (this does not apply to people working in industry).

https://www.prstatistics.com/course/r-package-design-and-development-and-reproducible-data-science-for-biologists-rpkg01/

Please email oliverhoo...@prstatistics.com with inquiries

This course will be delivered by Dr. Cory Merow and Dr Andy Rominger
from the 16th - 20th September 2019 in Glasgow City Centre.

Course overview:
This course will help students develop professional R coding skills by
leading them through the process of making reproducible, sharable and
easily communicated software centered around developing fully
functional R packages and extensions and is thus applicable to any
biologists working in the field of marine mammals. In addition to teaching
traditional uses of R packages to share quantitative tools, we’ll also
show how R packages can be easily developed for individual research
projects to share reproducible results. To develop skills, we’ll build
several R packages full of useful and general utility functions that
will hone coding skills and teach coding tips through the design of
these functions. Each day, we’ll reserve time for open work sessions
where students can receive mentoring while applying new skills to
developing their own application specific package or refining the
packages we’re developing for the course.

Intended Audience:
Anyone wanting to make their data science work accessible,
reproducible and usable by others (the importance of specific R
packages has grown considerable now that they are frequently cited in
peer reviewed literature). This can include researches developing
their own quantitative tools or those interested in taking the next
step in making their research projects fully reproducible and easily
shared.

Course program:

Monday 16th – Classes from 09:30 to 17:30
We’ll begin with polishing core skills in the creation, documentation
and distribution of code:
Writing functions
Making your code reproducible by documenting it with RMarkdown and ROxygen
Making your first package, breaking it, then fixing it
Package structure

Tuesday 17th – Classes from 09:30 to 17:30
Next we dive into specifics critical for the success of collaborative,
reproducible and sharable projects:
Principles of software development and reproducible projects
Writing useful documentation and examples
Error handling
Collaboration with git and GitHub

Wednesday 18th – Classes from 09:30 to 17:30
We will continue learning about the details that help to make a
package robust to different use cases:
Dependencies, and achieving independency
Unit Testing
Vignettes
The rules of CRAN and GitHub

Thursday 19th – Classes from 09:30 to 17:30
By now students will have fulling functioning, collaboratively
produced, and reproducible R packages. We now turn to two key aspects
of software usability: its computational burden, and its cognitive
burden. Put simply, we will focus today on making code computationally
fast and easy for users to quickly and intuitively understand.
Writing fast code
Profiling code for speed
S3 and S4 objects

Friday 20th – Classes from 09:30 to 16:00
On the final day we will culminate our software development by
learning and implementing powerful ways to share our projects with a
large audience.
Adding a shiny web app to a project
Publishing your own package

Email oliverhoo...@prstatistics.com

Check out our sister sites,
www.PRstatistics.com (Ecology and Life Sciences)
www.PRstatistics.com/consultancy (Statistical and bioinformatics
consultancy in all fields)
www.PRinformatics.com (Bioinformatics and data science)
www.PSstatistics.com (Behaviour and cognition)

1. September 2nd – 6th 2019
APPLIED METHODS FOR ANALYSING CAPTURE-RECAPTURE (MARK-RECAPTURE) DATA
USING SPATIALLY EXPLICIT AND NON-SPATIAL TECHNIQUES (MARK01)
Glasgow, Scotland, Dr. Joanne Potts, Dr. David Borchers
https://www.prstatistics.com/course/applied-methods-for-analysing-capture-recapture-mark-recapture-data-using-spatially-explicit-and-non-spatial-techniques-mark01/

2. September 9th – 13th 2019
GENERALISED LINEAR (MIXED) (GLMM), NONLINEAR (NLGLM) AND GENERAL
ADDITIVE MODELS (MIXED) (GAMM) (GNAM01)
Glasgow, Scotland, Dr. Mark Andrews
https://www.psstatistics.com/course/generalised-linear-glm-nonlinear-nlglm-and-general-additive-models-gam-gnam01/

3. September 16th – 20th 2019
STRUCTURAL EQUATION MODELS, PATH ANALYSIS, CAUSAL MODELLING AND LATENT
VARIABLE MODELS USING R (SMPA01)
Glasgow, Scotland, Dr. Mark Andrews
https://www.psstatistics.com/course/structural-equation-modelling-and-path-analysis-smpa01/

4. September 16th – 20th 2019
R PACKAGE DESIGN AND DEVELOPMENT AND REPRODUCIBLE DATA SCIENCE FOR
BIOLOGISTS (RP

[MARMAM] Potomac-Chesapeake Dolphin Project Field Assistant Ad

[Ann-Marie Jacoby]

Potomac-Chesapeake Dolphin Project Field Assistant Ad


The Potomac-Chesapeake Dolphin Project (PCDP) is seeking two dedicated research 
assistants for the upcoming fall field season (September 3rd to October 23rd, 
2019) in Heathsville, Virginia, USA. The PCDP was established in 2015 by 
Professor Janet Mann of Georgetown University. The PCDP’s mission is to better 
understand and protect bottlenose dolphins (Tursiops truncatus) in the 
Chesapeake Bay and greater western North Atlantic Ocean. Despite being the 
largest, and most populated estuary in the US, almost nothing is known about 
bottlenose dolphins in the Chesapeake. Yet, reports of dolphins in the area 
date back to the 1800s, with sightings as close as 13km from the US’ capitol, 
Washington, DC. This field season is part of an ongoing PhD project studying 
the populations dynamics, behavior, and historical presence of bottlenose 
dolphins in the Potomac River-Chesapeake Bay area.

Field work is demanding and requires long hours both on and off the water. 
There is no guarantee of seeing dolphins on a daily basis given their seasonal 
presence. However, when dolphins are sighted, there can be well over 100 in a 
group and spending time with them is incredibly fun and rewarding. Field 
assistants will gain valuable research experience. We particularly encourage 
those interested in pursuing graduate school in marine mammalogy to apply.


Timeframe:
~2 months


Field site:
Heathsville, Virginia, USA.

Heathsville is approximately 200km south east of Washington, D.C. in the 
Northern Neck of Virginia. Our field site is located where the Potomac River 
meets the Chesapeake Bay. Even though Heathsville is in relatively close 
proximity to DC, Heathsville is remote. We do have a fieldhouse with 
electricity, water, limited cell phone service, and limited internet. Housing 
will be provided, and the research team will share cooking and cleaning 
responsibilities in a communal kitchen. We eat a predominantly vegetarian diet.

Job responsibilities:

Research assistants will help collect transect and behavioral surveys on 
bottlenose dolphins. Boat work is dependent on weather, but even on windy days 
we need to be ready to pack up and quickly get out on the water if the wind 
drops. Days on the water can be consecutive, long, and tiring in variable 
environmental conditions (often very hot and humid conditions). Days on land 
require extensive, and tedious, data entry and processing.

Most of your time will be spent:
-Searching for and spotting dolphins
-Driving the boat

-Scribing data during surveys
-Entering transect surveys and coding photographs on the computer

-Doing basic maintenance and equipment prep and cleaning

Qualifications:
The ideal candidate will be a recent graduate with a science background and a 
genuine interest in marine mammal science and behavior. This position is well 
suited for recent graduates of marine biology, animal behavior, zoology, 
ecology, or similar fields looking to gain additional analytical and in-field 
experience. Applicants must be able to work closely with a small team (3 
people). We not only work together, but also live, cook, and eat together, so 
being mature and a strong team player is critical.

The candidate must:

-Possess basic computer skills
-Be detail oriented, flexible, and patient
-Possess excellent verbal and communication skills
-Work well both independently and in a team
-Be fluent in English
-Have prior research experience (preferably fieldwork)
-Be comfortable on a small boat
-Be prepared to work long, consecutive days, including weekends

The most essential qualifications are that you are flexible, conscientious, and 
hard-working, and are excited about the research.

Salary/funding:

This is an unpaid, volunteer position. However, all living expenses (housing, 
food, and internet) will be fully covered by the project. If you are unable to 
pay for domestic travel to and from the field site due to any student loans, or 
other moderate monthly expenses, that could prevent you from accepting this 
position, please apply anyway. If you are selected, we may be able to use other 
sources of funding to cover those expenses so that you can take the job. We 
particularly want to encourage candidates from groups that are underrepresented 
in STEM fields to apply.


If interested please email Ann-Marie Jacoby at 
am...@duke.edu with the subject line Research Assistant 
Last_Name. Application review will begin immediately, and candidates will be 
evaluated until the position is filled.


In the email, please include:
1. A cover letter describing your research interests, the skills and 
strengths that you will bring to the position, and what you hope to gain from 
the project and apply to your career. Please list the full range of your 
skills, both practical (boat handling, photography, etc.) and academic 
(statistics, computer programming, etc.).
2. CV

3. A copy of

[MARMAM] Ocean Sciences Meeting 2020 session: Climate Impacts on Marine Species

[Erin Meyer-Gutbrod]

Dear Colleagues,

The 2020 Ocean Sciences Meeting <
https://www2.agu.org/ocean-sciences-meeting/> will take place 16-21
February 2020 in San Diego, California.  We are chairing a new session
entitled "Climate Impacts on Marine Species" (PC002) <
https://agu.confex.com/agu/osm20/prelim.cgi/Session/85723>. This session is
an opportunity to exchange ideas about natural and anthropogenic climate
effects on marine species. We welcome studies that focus on a wide variety
of taxa, including fish, marine mammals, seabirds, corals, invertebrates
and plankton. We also welcome research on adopting fishery and/or marine
conservation policies in response to climate impacts. Please consider
submitting an abstract: <
https://agu.confex.com/agu/osm20/pc/papers/index.cgi?sessionid=85723>.
Abstracts are due by 11 September 2019.  More information on the session is
below.

Topic: Past, Present and Future Climate
Title: Climate impacts on marine species
Session ID: PC002

The marine environment is disproportionately impacted by climate change, as
evidenced through increasing water temperature, ocean acidification,
deoxygenation, rising sea levels, shifting circulation patterns and
increased storm activity. We invite presentations that explore the observed
or modeled response of marine organisms to climate variability or climate
change. Recent studies have revealed climate-mediated declines in some
marine species, while others have shown remarkable resilience to climate
change. For example, Arctic sea ice loss threatens species that rely on ice
for habitat such as polar bears and ringed seals, whereas tuna species that
target moderate sea surface temperatures may experience range expansion.
Ecological impacts can derive from changes in physiology, bioenergetics,
abundance, distribution, habitat, community structure, reproduction,
behavior, and phenology. A wide range of marine organisms will be
considered, including invertebrates, fish, reptiles, mammals, and sea
birds. We also invite presentations that explore climate impacts on marine
fisheries in terms of spatial distribution, changing target species and/or
gear type, or simply the challenges faced by fisheries management in a
changing climate. This session will showcase observed and predicted
responses of marine organisms to climate change and provide a venue for
researchers to contrast climate-driven phenomena across regions and taxa.

Erin Meyer-Gutbrod; University of California, Santa Barbara; e...@ucsb.edu
Vincent S Saba; NOAA National Marine Fisheries Service;
vincent.s...@noaa.gov
Kristin Liisa Laidre; Polar Science Center; klai...@uw.edu
Barbara Muhling; University of California, Santa Cruz;
barbara.muhl...@noaa.gov

-- 
Erin Meyer-Gutbrod, Ph.D.
http://meyer-gutbrod.weebly.com/

Marine Science Institute; Rm 3405
University of California, Santa Barbara
Santa Barbara, CA 93106-6150

eringutb...@gmail.com
216-548-9082
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[MARMAM] Recruiting - 3 PhD Opportunities

[Michelle Shero]

Recruiting 3 PhD students at: Woods Hole Oceanographic Institution, Texas Tech 
University, and University of Nevada Las Vegas  

in Marine Mammal Physiology, Behavior, and Genetics

We are seeking PhD candidates to work on an NSF-funded project using Weddell 
seals in McMurdo Sound, Antarctica as a model to examine why some individuals 
within populations produce more offspring than others. The successful 
candidates will be part of a highly-collaborative team that aims to distinguish 
which plastic (physiologic and behavioral) and fixed (genetic) traits make some 
‘robust’ female Weddell seals particularly successful at producing pups 
year-after-year, while other ‘frail’ females produce far fewer pups throughout 
their lifetime than the population’s average. The positions ideally would begin 
Fall 2020, but it would be possible to start later. Student research projects 
will reflect program needs in the following core fields, but will also be 
tailored to student interest. 

Physiology: One student will focus on the physiological factors that impact 
energy dynamics, aerobic capacity, and reproductive success so experience with 
biochemistry/molecular labwork is a plus. Example projects include studying 
female-to-pup energy transfer during lactation in ‘robust’ vs ‘frail’ female 
Weddell seals, links between female physiologic dive capacities and her pup’s, 
and differences in female reproductive phenology (ovulation timing, pregnancy 
rates, pregnancy loss) and hormones between ‘robust’ and ‘frail’ seals. This 
student would be housed at Woods Hole Oceanographic Institution’s Biology 
Department, in a joint-program with MIT, advised by Dr. Michelle Shero 
(www.shero-lab.com ). Details on the WHOI/MIT joint 
PhD program and admission criteria can be found at 
http://mit.whoi.edu/program-description 
, applications due Dec 15.

Behavior & Bioenergetics: One student will focus on year-round foraging 
behavior and the impact this has on activity budgets and bioenergetics, so any 
prior modeling or programming experience would be viewed favorably. Example 
projects include studying female-pup pair dive behavior during lactation, 
differences in summer/winter dive behavior between ‘robust’ and ‘frail’ seals, 
impacts of physiology on post-weaned pup dive behavior, and developing a 
bioenergetics model to identify crucial deviations in how ‘robust’ vs ‘frail’ 
seals navigate critical life history events. This student would be housed at 
Texas Tech University’s Department of Biological Sciences with Dr. Jennifer 
Burns (http://burnslab.wix.com/burnslab ). 
Prospective student information can be found at 
https://www.depts.ttu.edu/biology/academics/graduate/prospective-students/ 
, 
applications due Jan 15.

Genomics: One student will focus on the inherent genomic differences between 
‘robust’ and ‘frail’ Weddell seals, so experience with bioinformatics analysis 
would be an asset. Example projects include identifying genetic variants in 
genes responsible for energy allocation, aerobic scope, and fertility between 
Weddell seal cohorts through whole-genome sequencing. This student would also 
perform experiments to demonstrate that genetic variants ultimately have 
functional effects on animal phenotype (i.e., transcription, translation), and 
there is additional opportunity for cell culture experiments. This student 
would be advised by Dr. Allyson Hindle 
(https://www.researchgate.net/profile/Allyson_Hindle 
) at the University of 
Nevada Las Vegas, and would also work closely with Dr. Brandon Briggs 
(University of Alaska Anchorage; 
https://www.uaa.alaska.edu/academics/college-of-arts-and-sciences/departments/biological-sciences/faculty/briggs.cshtml
 
).
 Interested students should see: 
https://www.unlv.edu/degree/phd-biological-sciences 
; application deadline is 
Jan 15.

Preference will be given to highly motivated candidates with a Bachelor of 
Science or Master of Science degree in biology or closely related field, who 
have a strong academic record, and that enjoy working both in the laboratory 
and field. Candidates must be physically fit, able to work long hours outdoors 
in the cold, able to pass medical and dental screening criteria for long 
deployments in remote field locations and be the holder of a valid passport 
(U.S. or other). Prior laboratory and/or field research in ecology of mammals 
is a plus. The successful applicants will spend 2-4 months in the field at 
McMurdo Station, Antarctica, each year. The grant/institutions will provide 
student stipend and tuition, and students will be e