[MARMAM] New publication announcement: North Pacific Humpback Whale Photo-ID collaborative dataset

[Ted Cheeseman]

Dear friends of whales and photo-ID automation,

On behalf of my 68 co-authors(!!), I am pleased to announce the open access 
publication in Scientific Reports of the second paper to come from our broad 
collaboration:
A collaborative and near-comprehensive North Pacific humpback whale photo-ID 
dataset

Abstract
We present an ocean-basin-scale dataset that includes tail fluke photographic 
identification (photo-ID) and encounter data for most living individual 
humpback whales (Megaptera novaeangliae) in the North Pacific Ocean. The 
dataset was built through a broad collaboration combining 39 separate curated 
photo-ID catalogs, supplemented with community science data. Data from 
throughout the North Pacific were aggregated into 13 regions, including six 
breeding regions, six feeding regions, and one migratory corridor. All images 
were compared with minimal pre-processing using a recently developed image 
recognition algorithm based on machine learning through artificial 
intelligence; this system is capable of rapidly detecting matches between 
individuals with an estimated 97-99% accuracy. For the 2001 to 2021 study 
period, a total of 27,956 unique individuals were documented in 157,350 
encounters. Each individual was encountered, on average, in 5.6 sampling 
periods (i.e., breeding and feeding seasons), with an annual average of 87% of 
whales encountered in more than one season. The combined dataset and image 
recognition tool represents a living and accessible resource for collaborative, 
basin-wide studies of a keystone marine mammal in a time of rapid ecological 
change.


Available here: https://www.nature.com/articles/s41598-023-36928-1, or I’m 
happy to send a pdf 

Citation: Cheeseman, T., Southerland, K., Acebes, J.M. et al. A collaborative 
and near-comprehensive North Pacific humpback whale photo-ID dataset. Sci Rep 
13, 10237 (2023). https://doi.org/10.1038/s41598-023-36928-1

Yay whales!

:) Ted
—
Ted Cheeseman
t...@happywhale.com
www.Happywhale.com
https://www.facebook.com/happywhales/


Read our recent publications - humpback whale automated image recognition: 
https://rdcu.be/cCOtw and humpbacks of the North Pacific: https://rdcu.be/dfdPF

** know your whales :) **

—
I live and play on unceded lands of the Ohlone.




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[MARMAM] New publication announcement

[Florencia Vilches]

New publication: Long-term photo-ID, telemetry, and citizen science on
southern right whales (Florencia Vilches)

Dear MARMAM community,

We are excited to share our new publication, "Life Histories of
Satellite-Tracked Southern Right Whales Through Photo-Identification and
Citizen Science in Patagonia, Argentina" by Florencia O. Vilches, Mariano
Sironi, Alexandre N. Zerbini, Santiago J. Fernández, Marcela M. Uhart, and
Victoria J. Rowntree. Publication link:
https://doi.org/10.1578/AM.49.2.2023.167

In this note, we show how a 5-decade photo-identification study on
Patagonian southern right whales can integrate scientific research with
whale watching and citizen science and contribute relevant information to
enhance a satellite telemetry study.

Please do not hesitate to contact me at florencia.vilc...@icb.org.ar with
any questions regarding our work.

All the best,
Florencia


*Florencia Vilches *| she/hers/ella

Fulbright Scholar

Ph.D. Student | University of California, Santa Cruz | Costa
& Beltran 
 Labs
Researcher | Instituto de Conservación de Ballenas

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[MARMAM] New publication announcement: Evidence of stereotyped contact call use in narwhal (Monodon monoceros) mother-calf communication

[Audra Ames]

Dear colleagues,

On behalf of myself and my co-authors, we are pleased to announce the 
publication of our new paper in PLoS ONE.

Ames AE, Blackwell SB, Tervo OM, Heide-Jørgensen MP (2021) Evidence of 
stereotyped
contact call use in narwhal (Monodon monoceros) mother-calf communication. PLoS 
ONE 16(8):
e0254393. https://doi.org/10.1371/journal.pone.0254393

Abstract:

Narwhals (Monodon monoceros) are gregarious toothed whales that strictly reside 
in the
high Arctic. They produce a broad range of signal types; however, studies of 
narwhal vocalizations
have been mostly descriptive of the sounds available in the species’ overall 
repertoire.
Little is known regarding the functions of highly stereotyped mixed calls (i.e.,
biphonations with both sound elements produced simultaneously), although 
preliminary evidence
has suggested that such vocalizations are individually distinctive and function 
as contact
calls. Here we provide evidence that supports this notion in narwhal mother-calf
communication. A female narwhal was tagged as part of larger studies on the 
life history
and acoustic behavior of narwhals. At the time of tagging, it became apparent 
that the
female had a calf, which remained close by during the tagging event. We found 
that the narwhal
mother produced a distinct, highly stereotyped mixed call when separated from 
her calf
and immediately after release from capture, which we interpret as preliminary 
evidence for
contact call use between the mother and her calf. The mother’s mixed call 
production
occurred continually over the 4.2 day recording period in addition to a second 
prominent but
different stereotyped mixed call which we believe belonged to the narwhal calf. 
Thus, narwhal
mothers produce highly stereotyped contact calls when separated from their 
calves,
and it appears that narwhal calves similarly produce distinct, stereotyped 
mixed calls which
we hypothesize also contribute to maintaining mother-calf contact. We compared 
this
behavior to the acoustic behavior of two other adult females without calves, 
but also each
with a unique, stereotyped call type. While we provide additional support for 
individual distinctiveness across narwhal contact calls, more research is 
necessary to determine whether
these calls are vocal signatures which broadcast identity.

The publication can be open-accessed via 
https://doi.org/10.1371/journal.pone.0254393 or you can email a request for a 
PDF to aa...@oceanografic.org.

Many thanks for your interest in the article, and thank you to the PLOS ONE 
editors and the reviewers of the publication for their contributions to the 
finished article.

Best,
Audra

--
Audra Ames, Ph.D.
Research Scientist,
Fundación Oceanografic
T:  (+34) 96  1975526
Fundación Oceanogràfic de la Comunitat Valenciana
C/ Eduardo Primo Yúfera (Científic), 1B
46013 Valencia Spain


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[MARMAM] New publication announcement

[Shannon McCluskey]

Dear Marmam Community,

My co-authors and I are pleased to announce the publication of our paper on
stomach content and stable isotope analysis of a population of bottlenose
dolphins off the west coast of Australia.

McCluskey, S.M., K.R. Sprogis, J.M. London, L. Bejder, and N.R. Loneragan.
2021. ‘Foraging Preferences of an Apex Marine Predator Revealed through
Stomach Content and Stable Isotope Analyses’. *Global Ecology and
Conservation* 25 (January): e01396.
https://doi.org/10.1016/j.gecco.2020.e01396.


Abstract

Insights into the food habits of predators are essential for maintaining
healthy predator populations and the functioning of ecosystems. Stomach
content and stable isotope analyses were used to investigate the foraging
habits of an apex predator, the Indo-Pacific bottlenose dolphin (*Tursiops
aduncus*) in south-western Australia. A total of 2,594 prey items from 26
families were identified from the stomachs of 10 deceased stranded
dolphins. Fish otoliths from stomach contents were used to identify fish to
family or species level. Ninety-three percent of identified stomach
contents were perciforme fishes, however, perciformes comprised only 30% of
the catch during prey sampling. Gobiidae species, small fish generally
<100 mm in total length, were the most prevalent family identified in
dolphin stomachs, accounting for 82% of identified prey, yet Gobiidae
accounted for 12.7% of the catch during prey sampling. For stable isotope
analyses, tissue samples from 14 free-ranging dolphins were analyzed for
nitrogen (δ15N) and carbon (δ13C) ratios. From stable isotope analyses and
boat-based dolphin photo-identification surveys (n = 339, 2007–2011),
results indicated niche differentiation between coastal and inshore (bay
and estuarine habitat) dolphins. Carbon signatures showed that coastal
dolphins had a more pelagic diet compared to a benthic diet observed in the
inshore dolphins. Whereas, nitrogen signatures of inshore dolphins showed
higher nitrogen levels than coastal dolphins, likely attributed to feeding
on enriched prey typical of estuarian environments. Overall, these results
indicated that bottlenose dolphins in the study area were selective
foragers and that their foraging is specialized by the habitats most
frequently used.

The article is open-access and can be found here:
https://www.sciencedirect.com/science/article/pii/S2351989420309379?via%3Dihub

Thank you very much for sharing,
Shannon
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[MARMAM] New Publication announcement: Call types of Bigg's killer whales in western Alaska

[Deborah Sharpe]

My co-authors and I are pleased to announce the recent online release of the 
following article in Bioacoustics:

Call types of Bigg’s killer whales (Orcinus orca) in western Alaska: using 
vocal dialects to assess population structure.

Sharpe DL, Castellote M, Wade PR, and Cornick LA



ABSTRACT

Bigg’s killer whales (Orcinus orca; i.e. ‘transient’ ecotype), as apex 
predators, are important to the dynamics of marine ecosystems, but little is 
known about their population structure in western Alaska. Currently, all Bigg’s 
killer whales in western Alaska are ascribed to a single broad stock for 
management under the US Marine Mammal Protection Act. However, recent nuclear 
microsatellite and mitochondrial DNA analyses indicate that this stock is 
likely comprised of genetically distinct sub-populations. In accordance with 
what is known about killer whale vocal dialects in other locations, we used the 
spatial distribution of group-specific call types to investigate the population 
structure of Bigg’s killer whales in this part of Alaska. Digital audio 
recordings were collected from 33 Bigg’s killer whale encounters throughout the 
Aleutian and Pribilof Islands in the summers of 2001–2007 and 2009–2010. 
Recorded calls were qualitatively classified into discrete types and then 
quantitatively described using 12 structural and time-frequency measures. 
Resulting call categories were validated using a random forest approach. A 
total of 36 call types and subtypes were identified across the entire study 
area, and regional patterns of call type use revealed three distinct dialects 
which correspond to proposed genetic delineations. Our results suggest that 
there are at least three acoustically and genetically distinct sub-populations 
in western Alaska, and we present an initial catalogue for this area describing 
the regional vocal repertoires of Bigg’s killer whale call types.



For students, professors, and other scientists who are interested in our paper 
and have institutional access to articles, please use the following link: 
https://doi.org/10.1080/09524622.2017.1396562

For interested parties without the ability to circumvent pay-walls, a free copy 
can be obtained by clicking here: 
http://www.tandfonline.com/eprint/DwjAi5wHpjqzSFI5Ctzz/full . Please use this 
link only once.

If you are unable to access the full article through either of these channels, 
don’t hesitate to contact me directly: dlynnsha...@hotmail.com

Thank you for your interest,

Deborah L. Sharpe, MSc

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[MARMAM] New Publication Announcement

[Bromaghin, Jeffrey]

Colleagues,



I am pleased to announce the availability of an early-view paper that
presents a new model for the estimation of consumer diet composition using
quantitative fatty acid signature analysis, a method commonly used in
studies of marine species.



Citation:

Bromaghin, J. F., S. M. Budge, G. W. Thiemann, and K. D. Rode. 2017.
Simultaneous estimation of diet composition and calibration coefficients
with fatty acid signature data. Ecology and Evolution.
https://doi.org/10.1002/ece3.3179



Abstract:

Knowledge of animal diets provides essential insights into their life
history and ecology, although diet estimation is challenging and remains an
active area of research.  Quantitative fatty acid signature analysis
(QFASA) has become a popular method of estimating diet composition,
especially for marine species.  A primary assumption of QFASA is that
constants called calibration coefficients, which account for the
differential metabolism of individual fatty acids, are known.  In practice,
however, calibration coefficients are not known, but rather have been
estimated in feeding trials with captive animals of a limited number of
model species.  The impossibility of verifying the accuracy of feeding
trial derived calibration coefficients to estimate the diets of wild
animals is a foundational problem with QFASA that has generated
considerable criticism.  We present a new model that allows simultaneous
estimation of diet composition and calibration coefficients based only on
fatty acid signature samples from wild predators and potential prey.  Our
model performed almost flawlessly in four tests with constructed examples,
estimating both diet proportions and calibration coefficients with
essentially no error.  We also applied the model to data from Chukchi Sea
polar bears, obtaining diet estimates that were more diverse than estimates
conditioned on feeding-trial calibration coefficients.  Our model avoids
bias in diet estimates caused by conditioning on inaccurate calibration
coefficients, invalidates the primary criticism of QFASA, eliminates the
need to conduct feeding trials solely for diet estimation, and consequently
expands the utility of fatty acid data to investigate aspects of ecology
linked to animal diets.



Regards,

Jeff
---
Jeffrey F. Bromaghin, PhD
Research Statistician
USGS Alaska Science Center
Marine Ecosystems Office
4210 University Drive
Anchorage, AK 99508
907-786-7086
jbromag...@usgs.gov
*http://alaska.usgs.gov/science/biology/quantitative_ecology/index.php
*
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[MARMAM] New Publication Announcement

[Bromaghin, Jeffrey]

Colleagues,



I am pleased to announce the availability of an early-view paper that
describes a new R package, called qfasar, for the estimation of predator
diet composition using quantitative fatty acid signature analysis (QFASA).
QFASA is one of the most common methods of estimating diet composition for
marine species. The package incorporates traditional estimation methods and
several improvements drawn from a series of our recent methodology papers.



Citation:

Bromaghin, J. F. 2017. qfasar: quantitative fatty acid signature analysis
with R. Methods in Ecology and Evolution. doi: 10./2041-210X.12740.



Summary

1. Knowledge of predator diets provides essential insights into their
ecology, yet diet estimation is challenging and remains an active area of
research.

2. Quantitative fatty acid signature analysis (QFASA) is a popular method
of estimating diet composition that continues to be investigated and
extended. However, software to implement QFASA has only recently become
publicly available.

3. I summarize a new R package, qfasar, for diet estimation using QFASA
methods. The package also provides functionality to evaluate and
potentially improve the performance of a library of prey signature data,
compute goodness-of-fit diagnostics, and support simulation-based research.
Several procedures in the package have not previously been published.

4. QFASAR makes traditional and recently published QFASA diet estimation
methods accessible to ecologists for the first time. Use of the package is
illustrated with signature data from Chukchi Sea polar bears and potential
prey species.



Regards,

Jeff
---
Jeffrey F. Bromaghin, PhD
Research Statistician
USGS Alaska Science Center
Marine Ecosystems Office
4210 University Drive
Anchorage, AK 99508
907-786-7086
jbromag...@usgs.gov

*http://alaska.usgs.gov/science/biology/quantitative_ecology/index.php
*
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