[MARMAM] Ship-strike forecast (north coast British Columbia) + R package 'shipstrike'

[Eric Keen]

Dear colleagues,

On behalf of my coauthors and our long-time collaborators in the Gitga'at
First Nation, I share a new ship-strike study published this week as well
as a related R package, 'shipstrike', for applying our approach to other
study areas.

Eric Keen EM, Éadin O’Mahony, Linda Nichol, Brianna Wright, Chenoah Shine,
Benjamin Hendricks, Hermann Meuter, Hussein Alidina, Janie Wray (2023)
Ship-strike forecast and mitigation for whales in Gitga’at First Nation
territory. Endangered Species Research 51:31-58.
https://doi.org/10.3354/esr01244

Abstract:
As marine traffic increases globally, ship strikes have emerged as a
primary threat to many baleen whale populations. Here we predict
ship-strike rates for fin whales Balaenoptera physalus and humpback whales
Megaptera novaeangliae in the central territorial waters of the Gitga’at
First Nation (British Columbia, Canada), which face increases in existing
marine traffic as well as new liquified natural gas (LNG) shipping in the
next decade. To do so, we utilized Automatic Identification System (AIS)
databases, line-transect surveys, shore-based monitoring, whale-borne tags,
aerial drone-based focal follows, and iterative simulations. We predict
that by 2030, whale encounters will triple for most vessel types, but the
change is most extreme for large ships (length >180 m) in prime whale
habitat, in which co-occurrences will increase 30-fold. Ship-strike
mortalities are projected to increase in the next decade by 2.3x for fin
whales and 3.9x for humpback whales, to 2 and 18 deaths yr-1, respectively.
These unsustainable losses will likely deplete both species in the coastal
region of BC. Models indicate that the largest single source of mortality
risk in 2030 will be from the LNG Canada project. Of the mitigation options
we evaluated, a 10 knot speed ceiling for all large ships is potentially
effective, but the best measure for guaranteed mitigation would be seasonal
restrictions on LNG traffic. While certain data gaps remain, particularly
with respect to humpback whales, our predictions indicate that shipping
trends within Gitga’at waters will impact whale populations at regional
levels. We provide our analysis in the R package ‘shipstrike’.

The paper is open-access with Endangered Species Research:
https://www.int-res.com/articles/esr2023/51/n051p031.pdf

Link to supplemental material:
https://www.int-res.com/abstracts/esr/v51/p31-58/

Link to press release:
https://wwf.ca/media-releases/lng-ship-traffic-in-b-c-could-dramatically-increase-whale-deaths-study/

Link to 'shipstrike' package on Github:
https://github.com/ericmkeen/shipstrike

Link to package vignette:
https://ericmkeen.github.io/shipstrike/
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[MARMAM] Ship-strike encounter rate simulator: new publication

[Eric Keen]

Dear colleagues,

My coauthors and I are pleased to share the following article recently
published in *Ocean & Coastal Management*:

Keen, Eric M; Hendricks, Ben; Shine, Chenoah; Wray, Janie; Picard, Chris
R;  Alidina, Hussein M. (2022). A simulation-based tool for predicting
whale-vessel encounter rates. In Ocean & Coastal Management (Vol. 224, p.
106183). Elsevier BV. https://doi.org/10.1016/j.ocecoaman.2022.106183

Abstract ==
To understand the threat of ship strikes for marine predators such as
whales, quantitative tools are needed that measure specific impacts without
ignoring the many uncertain and stochastic elements of whale-vessel
interactions. We developed a tool that focuses on one particularly complex
aspect of the ship-strike problem: the encounter rate, the fraction of
co-occurrences (i.e., times that whales and vessels occur within the same
1-km2) that result in an imminent collision. This tool uses iterative
simulations, based in R, and basic inputs regarding marine traffic and
whale biology to predict the rate at which the precise courses of the whale
and the vessel intersect in space and time. The result of this simulator is
a spatially explicit probability distribution of encounter rates, which can
be summarized for reports as well as integrated into subsequent stages of a
ship-strike impact analysis. We explain the design of this tool, provide
its source code, and demonstrate its utility with four case applications.
First, we estimate encounter rates for fin whales (Balaenoptera physalus)
in Gitga'at First Nation waters (British Columbia, BC, Canada) and quantify
the differences in encounter rate between vessel classes. Second, we
predict encounter rates for the same area in 2030, by which time a new
shipping lane is slated to be established in Gitga'at territory,
highlighting the impact of shifting traffic composition vs. traffic volume.
Third, we assess the sensitivity of these estimates to changes in vessel
and whale characteristics, finding that vessel length is the most important
determinant of the encounter rate, followed by whale speed. Fourth, we
integrate the encounter rate estimator into a shipping impact assessment
for Gitga'at fin whales. Our predictions indicate that this decade's
traffic increase in Gitga'at waters alone could match Potential Biological
Removal for coastal BC fin whales. However, the assumptions underlying our
prediction require validation and further study. The encounter rate
simulator is available in the R package, “shipstrike”.

The article may be accessed at the link below, or by contacting me.
https://authors.elsevier.com/a/1ex4q3RKK-uDAk

A demo for the corresponding R package 'shipstrike' (available on GitHub)
can be found here:
https://ericmkeen.github.io/shipstrike/

Our special thanks to the Gitga'at First Nation for their collaboration and
support in this work.

Best wishes,
Eric Keen
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[MARMAM] Fin whales in the Great Bear Rainforest (British Columbia, CA)

[Eric Keen]

Colleagues,

On behalf of my co-authors, and with special recognition of our
collaborators in the Gitga'at First Nation, I share news of this recent
publication:

Keen EM, Pilkington J, O’Mahony É, Thompson K-L, Hendricks B, Robinson N,
Alidina H, Meuter. H, Picard CR, Wray J. (2021) Fin whales of the Great
Bear Rainforest: *Balaenoptera physalus velifera* in a Canadian Pacific
fjord system. PLoS ONE 16(9): e0256815.
https://doi.org/10.1371/journal.pone.0256815

Abstract
Fin whales (*Balaenoptera physalus*) are widely considered an offshore and
oceanic species, but certain populations also use coastal areas and
semi-enclosed seas. Based upon fifteen years of study, we report that
Canadian Pacific fin whales (*B*. *p*. *velifera*) have returned to the
Kitimat Fjord System (KFS) in the Great Bear Rainforest, and have
established a seasonally resident population in its intracoastal waters.
This is the only fjord system along this coast or elsewhere in which fin
whales are known to occur regularly with strong site fidelity. The KFS was
also the only Canadian Pacific fjord system in which fin whales were
commonly found and killed during commercial whaling, pointing to its
long-term importance. Traditional knowledge, whaling records, and citizen
science databases suggest that fin whales were extirpated from this area
prior to their return in 2005–2006. Visual surveys and mark-recapture
analysis documented their repopulation of the area, with 100–120 whales
using the fjord system in recent years, as well as the establishment of a
seasonally resident population with annual return rates higher than 70%.
Line transect surveys identified the central and outer channels of the KFS
as the primary fin whale habitat, with the greatest densities occurring in
Squally Channel and Caamaño Sound. Fin whales were observed in the KFS in
most months of the year. Vessel- and shore-based surveys (27,311 km and
6,572 hours of effort, respectively) indicated regular fin whale presence
(2,542 detections), including mother-calf pairs, from June to October and
peak abundance in late August–early September. Seasonal patterns were
variable year-to-year, and several lines of evidence indicated that fin
whales arrived and departed from the KFS repeatedly throughout the summer
and fall. Additionally, we report on the population’s social network and
morphometrics. These findings offer insights into the dynamics of
population recovery in an area where several marine shipping projects are
proposed. The fin whales of the Great Bear Rainforest represent a rare
exception to general patterns in this species’ natural history, and we
highlight the importance of their conservation.

A PDF of this paper is available open-source from PLoS ONE:
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0256815

Best wishes,

Eric Keen
ericmk...@gmail.com
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[MARMAM] catRlog, a new photo-ID project mgmt system in R

[Eric Keen]

Dear colleagues,

My coauthors and I are pleased to share news of the following publication:

Keen, E.M., Wren, J., O’Mahony, É., Wray, J. catRlog: a
photo-identification project management system based in R. Mamm Biol
(2021). https://doi.org/10.1007/s42991-021-00158-7

Abstract
Photo-identification (photo-ID) databases can comprise versatile troves of
information for well-studied animal populations and, when organized well
and curated carefully, can be readily applied to a wide range of research
questions, such as population abundance estimates, meta-population
connectivity and social network structure. To bring the potential impact of
photo-ID data within reach of a greater number of research groups, we
introduce an R-based photo-ID project management system, named catRlog. As
a computer directory with custom apps embedded throughout, catRlog serves
as a workflow organizer that simplifies, streamlines, and improves the
quality of photo-ID data processing. The system can be utilized by research
teams in a number of ways, ranging from automated formatting and printing
of a photo-ID catalog, to photo-ID matching, thereby creating and expanding
a historical catalog, to processing of identification data to generate
datasets necessary for site fidelity, mark–recapture, and social
association analyses. As an R-based tool, the apps are open-source,
cross-platform, readily customizable, and easily updated. catRlog has been
tested using photo-ID databases of humpback whales (Megaptera novaeangliae)
and fin whales (Balaenoptera physalus) within a mainland fjord system of
Pacific Canada, but is a generalized system useful for almost any photo-ID
project of any species in any habitat. A detailed user’s manual and example
dataset are provided.

This article is a contribution to the special issue of Mammalian Biology on
“Individual Identification and Photographic Techniques in Mammalian
Ecological and Behavioural Research: Methods, Applications and
Concepts”—Editors: Leszek Karczmarski, Stephen C.Y. Chan, Daniel I.
Rubenstein, Scott Y.S. Chui and Elissa Z. Cameron.

The paper and catRlog manual may be viewed here: https://rdcu.be/csdPC

The catRlog code lives here: https://github.com/ericmkeen/catRlog

Please contact me with any questions (ericmk...@gmail.com)

Best wishes,
Eric Keen
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[MARMAM] Humpback whale social structure in northern British Columbia

[Eric Keen]

Colleagues,

On behalf of my co-authors I am pleased to share the following publication:

Wray J, Keen EM, O’Mahony ÉN (2021) Social survival: Humpback whales
(*Megaptera
novaeangliae*) use social structure to partition ecological niches within
proposed critical habitat. PLOS ONE 16(6): e0245409.

Open access: https://doi.org/10.1371/journal.pone.0245409

*Abstract:*
Animal culture and social bonds are relevant to wildlife conservation
because they influence patterns of geography, behavior, and strategies of
survival. Numerous examples of socially-driven habitat partitioning and
ecological-niche specialization can be found among vertebrates, including
toothed whales. But such social-ecological dynamics, described here as
‘social niche partitioning’, are not known among baleen whales, whose
societies—particularly on foraging grounds—are largely perceived as
unstructured and incidental to matters of habitat use and conservation.
However, through 16 years of behavioral observations and
photo-identifications of humpback whales (*Megaptera novaeangliae*) feeding
within a fjord system in the Canadian Pacific (primarily within Gitga’at
First Nation waters), we have documented long-term pair bonds (up to 12
years) as well as a complex societal structure, which corresponds closely
to persistent patterns in feeding strategy, long-term site fidelity
(extended occupancy and annual rate of return up to 75%), specific
geographic preferences within the fjord system, and other forms of habitat
use. Randomization tests of network congruency and clustering algorithms
were used to test for overlap in patterns of social structure and habitat
use, which confirmed the occurrence of social niche partitioning on the
feeding grounds of this baleen whale species. In addition, we document the
extensive practice of group bubble net feeding in Pacific Canada. This
coordinated feeding behavior was found to strongly mediate the social
structure and habitat use within this humpback whale society. Additionally,
during our 2004–2019 study, we observed a shift in social network structure
in 2010–2012, which corresponded with environmental and demographic shifts
including a sudden decline in the population’s calving rate. Our findings
indicate that the social lives of humpback whales, and perhaps baleen
whales generally, are more complex than previously supposed and should be a
primary consideration in the assessment of potential impacts to important
habitat.

Lead author Janie Wray is the corresponding author for this paper:
ja...@bcwhales.org

Best wishes,
Eric Keen
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[MARMAM] Detection functions from shore

[Eric Keen]

Dear colleagues,

On behalf of my co-authors, I am pleased to announce the publication of the
following article in Wildlife Research.

Keen, E.M., J. Wray, B. Hendricks, É. O'Mahony, C.R. Picard, H. Alidina.
(2020) Determining marine mammal detection functions for a stationary
land-based survey site. Wildlife Research. https://doi.org/10.1071/WR19232

Pre-print PDF is available upon request.

Best wishes,
Eric Keen
ericmk...@gmail.com

ABSTRACT
Context: The shore-based survey is a common, non-invasive, and low-cost
method in marine mammal science, but its scientific applications are
currently limited. Such studies typically target populations whose
distributions are not random with respect to nearshore sites and involve
repeated scans of the same area from single, stationary platforms. These
circumstances prohibit the use of classic distance sampling techniques for
estimating animal densities or distributions, particularly the derivation
of a detection function that describes the probability of detecting targets
at various distances from the observer.

Aims: Here, we present a technique for estimating land-based detection
functions, as well as quantifying uncertainty in their parameterisation, on
the basis of the range-specific variability of observations from one scan
to the next.

Methods: This Bayesian technique uses Monte Carlo simulation to determine
the likelihood of thousands of candidate detection functions, then conducts
weighted sampling to generate a posterior distribution estimate of the
detection function parameterisation. We tested the approach with both
archival and artificial datasets built from known detection functions that
reflect whale and porpoise detectability.

Key results: When the base distribution of targets was random, the whale
detection function was estimated without error (i.e. the difference of the
median of the posterior and the true value was 0.00), and the porpoise
detection function was estimated with an error equal to 4.23% of the true
value. When the target base distribution was non-random, estimation error
remained low (2.57% for targets concentrated offshore, 1.14% when
associated with nearshore habitats). When applied to field observations of
humpback whales and Dall’s porpoises from a land-based study in northern
British Columbia, Canada, this technique yielded credible results for
humpback whales, but appeared to underestimate the detectability of Dall’s
porpoises.

Conclusion: The findings presented here indicate that this approach to
detection function estimation is appropriate for long-running surveys in
which scan regularity is high and the focus is on large, slow-moving, low
herd-size, and easily detectable species.

Implications: The derivation of a detection function is a critical step in
density estimation. The methodology presented here empowers land-based
studies to contribute to quantitative monitoring and assessment of marine
mammal populations in coastal habitats.
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[MARMAM] New publication: Day-night differences in fin whale ship-strike risk (California Current)

[Eric Keen]

Dear colleagues,

My co-authors and I are pleased to share news of a recent publication in
Frontiers in Marine Science:

Keen EM, Scales KL, Rone BK, Hazen EL, Falcone EA and Schorr GS (2019)
Night and Day: Diel Differences in Ship Strike Risk for Fin Whales
(Balaenoptera physalus) in the California Current System. Front. Mar. Sci.
6:730. doi: 10.3389/fmars.2019.00730

Link to paper (full open-access):
https://www.frontiersin.org/articles/10.3389/fmars.2019.00730/full

Abstract:
Collisions with ships (ship strikes) are a pressing conservation concern
for fin whales (Balaenoptera physalus) along western North America. Fin
whales exhibit strong diel patterns in dive behavior, remaining near the
surface for most of the night, but how this behavior affects ship-strike
risk is unknown. We combined diel patterns of surface use, habitat
suitability predictions, and ship traffic data to evaluate spatial and
temporal trends in ship-strike risk to fin whales of the California Current
System (CCS). We tested a range of surface-use scenarios and found that
both increased use of the upper water column and increased ship traffic
contribute to elevated ship-strike risk at night. Lengthening nights
elevate risk during winter throughout the CCS, though the Southern
California Bight experienced consistently high risk both day and night
year-round. Within designated shipping lanes, total annual nighttime strike
risk was twice daytime risk. Avoidance probability models based on ship
speed were used to compare the potential efficacy of speed restrictions at
various scales. Speed reductions within lanes may be an efficient
remediation, but they would address only a small fraction (13%) of overall
ship-strike risk. Additional speed restrictions in the approaches to lanes
would more effectively reduce overall risk.

Please contact me if you have any questions.

Best wishes,
Eric Keen
ericmk...@gmail.com

-- 
Eric M Keen <http://www.emkeen.org>

Biologist, Marine Ecology & Telemetry Research
Department of Earth & Environmental Systems, Sewanee: The University of the
South
Science Director, North Coast Cetacean Society
Editor, Aquatic Mammals Journal
Co-Founder, International Manatee Day
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[MARMAM] Publication: Fjord habitat use strategies of fin and humpback whales

[Eric Keen]

On behalf of my co-authors, I would like to bring the following publication
in *Marine Environmental Research* to your attention:

*Distinct habitat use strategies of sympatric rorqual whales within a fjord
system*
EM Keen, J Wray, J Pilkington, KL Thompson, CR Picard

Link to article 

*Abstract:*
We used ecosystem sampling during systematic surveys and opportunistic
focal follows, comparison tests, and random forest models to evaluate fin
whale (Balaenoptera physalus) and humpback whale (Megaptera novaeangliae)
habitat associations within an inland feeding ground (Kitimat Fjord System,
British Columbia, Canada). Though these species are sympatric and share a
common prey source, they were attuned to different aspects of the local
habitat. The fin whales were associated with habitat properties reminiscent
of the open ocean. Humpback whales, in contrast, were associated with
features more commonly associated with the inland waters of fjords. Fixed
habitat features, such as seafloor depth and distance from the fjord mouth,
were the most important predictors of fin whale presence, but fixed and
dynamic variables, such as surface properties, predicted humpback whale
presence with equal (moderate) success. With the exception of strong
salinity gradients for humpback whales, habitat conditions were poor
predictors of feeding state. Fin whales practiced a spatially confined,
seasonally stable, and thus more predictable use of certain channels within
the fjord system. These findings are compatible with site loyal behavior,
which is interesting in light of the species' historical, unique use of
this fjord system. The relatively lackluster performance of
humpback-habitat models, coupled with the importance of oceanographic
properties, makes the humpback's habitat use strategy more uncertain. The
fact that two sympatric species sharing a common prey source exhibited
different habitat use strategies suggests that at least one species was
informed by something in addition to prey. Given that the two species are
attuned to different aspects of the fjord habitat, their responses to
habitat changes, including anthropogenic impacts, would likely be different
in both nature and degree. Our findings highlight the value of comparative
studies and the complexity of rorqual habitat use, which must be understood
in order for critical habitat to be identified and protected.


--
Eric M Keen

PhD, Scripps Institution of Oceanography
Visiting Professor, Sewanee: The University of the South
Science Director, North Coast Cetacean Society
Biologist, Marine Ecology & Telemetry Research
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[MARMAM] Announcing Whale Song!, the peer-reviewed children's album about cetaceans

[Eric Keen]

Dear MARMAM,

I'm happy to announce the release of my educational children's album
about whales
and dolphins:

WHALE SONG! Groovin' Lessons on the Cetacea for kids and their
grown-ups is the first-ever peer-reviewed children's album about
cetaceans.  Packed with original, fact-filled, toe-tappin' tunes, Whale
Song! blends science and imagination into a lyrical adventure for the
whole family!  It's an ideal gift for kids of all ages -- the perfect way
to inspire youngsters to know and care more about what we do.

CDs are available now at: http://www.cdbaby.com/cd/erickeen.

Or download the album from
iTunes: 
http://itunes.apple.com/us/album/whale-song!-groovin-lessons/id485603165?ign-mpt=uo%3D4

or
Facebook: 
http://www.facebook.com/pages/Whale-Song/119217438194317?sk=app_155326481208883


For more info and reviews from leading whale scientists, see below.

Best wishes to all,
Eric Keen
Scripps Institution of Oceanography

~~
Peer Review for Whale Song!:

Baby Beluga move over! Here is a new cetacean kids song -- not just
one song but a whole album!  What I liked most was that these songs were
fun and funny for kids but also had interesting lyrics for adults and
even whale scientists (not sure if they qualify as adults). Who would think
you could get something like “their vestigial features show it” into
a children’s song and pull it off? There are valuable conservation themes,
vocabulary building, and educational aspects that the songs provide while
making it entertaining. This is a fun album for all ages through adults and
a must-have for budding whale scientists.
  -- John Calambokidis, director of the Cascadia Research Collective

I subjected Eric's songs to the toughest critics I could muster: my 4
yr old and 1 yr old. Within seconds they were laughing, dancing,
and clapping along. They had great fun...The problem I have now is that my
4 yr old is continuously pestering me, 'Can I hear another funny
song please?'
   -- Trevor Branch, PhD, UW Professor

Fun. Fun! FUN! I listened carefully to the whole thing because I
didn't want to miss a single chorus or bad pun. Its creative, educational,
and (did I mention?) fun.  I recommend it to cetacean biologists of all
ages, but especially those who will be getting their degrees in 20 years.
As a whale biologist with over 30 years of experience, I can testify that
he got all the science right. But none of that would matter to kids unless
it was also a hoot. Listen, it will make you smile.
-- Jay Barlow, PhD, Scripps Institution of Oceanography; NOAA Southwest
Fisheries Science Center

As someone who studies whale songs for a living, I was as enchanted
by these songs ABOUT whales as I am by songs sung BY whales. Eric's work
here is funny, catchy, and spot-on scientifically. Kids, adults, and
marine mammal scientists alike will find themselves singing along to the
'Whale BCs' , tracing the evolution of whales from land to water and back
again in song, and learning about a species most of us have never heard of,
the ole' walrus whale.
 -- Kate Stafford, PhD, whale acoustician, UW

~~
Special thanks goes my sister, Sara, to whom this album is dedicated.
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