[MARMAM] New Publication: spatiotemporal variability in resident killer whale diets

[Amy Van Cise]

Dear MARMAM,

My co-authors and I are excited to share our recent work describing
spatiotemporal diet variability in Pacific resident killer whales:

Van Cise, A. M., Hanson, M. B., Emmons, C., Olsen, D., Matkin, C. O.,
Wells, A. H., & Parsons, K. M. (2024). Spatial and seasonal foraging
patterns drive diet differences among north Pacific resident killer whale
populations. Royal Society Open Science, 11(9), rsos240445.
https://doi.org/10.1098/rsos.240445

Abstract:
Highly social top marine predators, including many cetaceans, exhibit
culturally learned ecological behaviours such as diet preference and
foraging strategy that can affect their resilience to competition or
anthropogenic impacts. When these species are also endangered, conservation
efforts require management strategies based on a comprehensive
understanding of the variability in these behaviours. In the northeast
Pacific Ocean, three partially sympatric populations of resident killer
whales occupy coastal ecosystems from California to Alaska. One population
(southern resident killer whales) is endangered, while another (southern
Alaska resident killer whales) has exhibited positive abundance trends for
the last several decades. Using 185 faecal samples collected from both
populations between 2011 and 2021, we compare variability in diet
preference to provide insight into differences in foraging patterns that
may be linked with the relative success and decline of these populations.
We find broad similarities in the diet of the two populations, with
differences arising from spatiotemporal and social variability in resource
use patterns, especially in the timing of shifts between target prey
species. The results described here highlight the importance of
comprehensive longitudinal monitoring of foraging ecology to inform
management strategies for endangered, highly social top marine predators.

The paper is open-access and can be downloaded directly from RSOS
, from ResearchGate
,
or from my lab's website .

Warm regards,
Amy

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D.
(she/her/hers)

Assistant Professor
Whale and Dolphin Ecology Lab 
University of Washington | School of Aquatic and Fisheries Sciences
1122 NE Boat St, Box 355020
Seattle, WA 98105
Office: SAFS 216B
206-221-6118

Need to meet with me? Let's find a time
.

Where is Amy? [Spring 2024 edition]**
Monday: UW campus
Tuesday: UW campus
Wednesday: UW campus
Thursday: hiding (focus day)
Friday: UW campus

**This is not exact. If you can't find me, shoot me an email and I will get
back to you.

"My paper was one long gigantic blunder from beginning to end."
-Charles Darwin
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[MARMAM] 3rd Marine Mammal eDNA Workshop at SMM2024

[Amy Van Cise]

Dear MARMAM,

We are excited to announce the 3rd Marine Mammal eDNA Workshop
<https://www.smmconference.org/workshops/#1647455659326-59b2adc5-38db> at
the 2024 SMM Biennial conference, which will be held as a full-day workshop
on Saturday, November 9.

The 3rd Marine Mammal eDNA workshop will bring together early-career and
established researchers interested in applying emerging techniques in
environmental DNA (eDNA) to marine mammal species. Environmental DNA
approaches to characterize organismal DNA from marine and freshwater have
shown promise for accelerating marine conservation, especially for cryptic,
rare, and logistically challenging species.

Following the success of the first two eDNA workshops held at SMM,
significant research effort has resulted in novel insight and growth of the
field over the last two years. Researchers will share methods developments
and lessons learned from recent eDNA work and explore priority areas for
further development in the next two years. Participants will then engage in
small-group discussion via breakout groups on relevant topics such as
experimental design and best practices for eDNA sampling in the field,
important considerations for eDNA sample processing, developing methods to
move toward quantitative metabarcoding and data analysis, and developing
methods for the use of eDNA beyond species detection – e.g. abundance
estimation or stock identification, and others based on a pre-survey of
participant interests. Throughout the workshop, we aim to broadly address
both the challenges and opportunities that eDNA affords for marine mammal
science.

*Note that we are currently researching options for a virtual component,
and will send a separate announcement if we are able to make this
available.*

We look forward to seeing you there!

Warm Regards,
Amy Van Cise, Kim Parsons, Julia Sunnarborg, Kristina Cammen, and Maggie
Hunter

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D.
(she/her/hers)

Assistant Professor
Whale and Dolphin Ecology Lab <http://amyvancise.com>
University of Washington | School of Aquatic and Fisheries Sciences
1122 NE Boat St, Box 355020
Seattle, WA 98105
Office: SAFS 216B
206-221-6118

Need to meet with me? Let's find a time
<https://calendar.app.google/6S7FAok44L6n2TpF7>.

Where is Amy? [Spring 2024 edition]**
Monday: UW campus
Tuesday: UW campus
Wednesday: UW campus
Thursday: hiding (focus day)
Friday: UW campus

**This is not exact. If you can't find me, shoot me an email and I will get
back to you.

"My paper was one long gigantic blunder from beginning to end."
-Charles Darwin
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[MARMAM] New publication: Best practices for sample collection, processing, and storage in the 'omics era

[Amy Van Cise]

Dear MARMAM,

My coauthors and I are happy to share a new review paper published in
Marine Mammal Science that synthesizes current scientific literature to
provide a set of guidelines for the field collection, processing, and
long-term storage of biological samples for use in existing and emerging
'omics research techniques.

Van Cise AM, AD Switzer, A Apprill, CD Champagne, PM Chittaro, NK Dudek, MR
Gavery, BL Hancock-Hanser, AC Harmon, AL Jaffe, NM Kellar, CA Miller, PA
Morin, SE Nelms, KM Robertson, IR Schultz, E Timmins-Schiffman, E Unal, KM
Parsons. 2024. Best practices for preserving marine mammal biological
samples in the ‘omics era. Marine Mammal Science 2024:e13148
.

*Abstract:* The recent rise of ‘omics and other molecular research
technologies alongside improved techniques for tissue preservation have
broadened the scope of marine mammal research. Collecting biological
samples from wild marine mammals is both logistically challenging and
expensive. To enhance the power of marine mammal research, great effort has
been made in both the field and the laboratory to ensure the scientific
integrity of samples from collection through processing, supporting the
long-term use of precious samples across a broad range of studies. However,
identifying the best methods of sample preservation can be challenging,
especially as this technological toolkit continues to evolve and expand.
Standardizing best practices could maximize the scientific value of
biological samples, foster multi-institutional collaborative efforts across
fields, and improve the quality of individual studies by removing potential
sources of error from the collection, handling, and preservation processes.
With these aims in mind, we summarize relevant literature, share current
expert knowledge, and suggest best practices for sample collection and
preservation. This manuscript is intended as a reference resource for
scientists interested in exploring collaborative studies and preserving
samples in a suitable manner for a broad spectrum of analyses, emphasizing
support for ‘omics technologies.

A pdf copy of the paper can be found on ResearchGate
.
Please don't hesitate to get in touch if you have any questions.

Warm Regards,
Amy

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D.
(she/her/hers)

Assistant Professor
Whale and Dolphin Ecology Lab 
University of Washington | School of Aquatic and Fisheries Sciences
1122 NE Boat St, Box 355020
Seattle, WA 98105
Office: SAFS 216B
206-221-6118

Need to meet with me? Let's find a time
.

Where is Amy? [Spring 2024 edition]**
Monday: UW campus
Tuesday: UW campus
Wednesday: UW campus
Thursday: hiding (focus day)
Friday: UW campus

**This is not exact. If you can't find me, shoot me an email and I will get
back to you.

"My paper was one long gigantic blunder from beginning to end."
-Charles Darwin
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[MARMAM] Job Opening - Molecular Genetics Technician

[Amy Van Cise]

Dear MARMAM,

The University of Washington Whale and Dolphin Ecology lab
 and the Genetics and Evolution lab

at NOAA Northwest Fisheries Science Center are seeking to hire a Research
Scientist/Engineer II - Molecular Genetics Technician

to support projects assessing marine mammal and fish population genetics
using a wide variety of genetic lab techniques. The position will primarily
support the genetic analysis of killer whale diets using fecal samples,
with additional opportunities to work on various fish and marine mammal
genetics projects expected.

The position will require the use of a wide range of molecular genetic
techniques, as well as bioinformatic sequence processing and some data
summary analyses, with opportunities to contribute to reports and
manuscripts. Maintaining an inventory of archived biological samples and
generated data (and metadata) will require strong organizational skills,
familiarity with relational databases and the ability to work
collaboratively as part of a diverse team.  This position is primarily
laboratory based but may involve limited fieldwork.

The desired start date is January 2024, and the position is funded for 12
months with additional time based on availability of funding, through the
School of Aquatic and Fisheries Sciences at the University of Washington.
The successful candidate will work in Seattle, WA at NOAA’s Northwest
Fisheries Science Center.

Salary range: $5,772 - $6,642/month, depending on experience
Location: Seattle, WA
Time Period: Jan - Dec 2024, with option to renew dependent on funding

Visit the job posting

at UW for more information and to apply.

Feel free to contact me (avanc...@uw.edu) or Kim Parsons (
kim.pars...@noaa.gov) with any questions about the position.

Cheers,
Amy

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D.
(she/her/hers)

Assistant Professor
Whale and Dolphin Ecology Lab 
University of Washington | School of Aquatic and Fisheries Sciences
1122 NE Boat St, Box 355020
Seattle, WA 98105
Office: SAFS 216B
206-221-6118

"My paper was one long gigantic blunder from beginning to end."
-Charles Darwin
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[MARMAM] Postdoc Opportunity: marine mammal spatial analysis using eDNA at the University of Washington

[Amy Van Cise]

Hello MARMAM,

We are looking for a postdoctoral scholar to join us at the University of
Washington School of Aquatic and Fisheries Sciences in Seattle, WA.

This position is funded to work on a new grant from the Office of Naval
Research as part of the Multidisciplinary University Research Initiative
(MURI) awards. The project, entitled "MMARINeDNA: Marine Mammal Remote
detection via INnovative environmental DNA sampling," aims to improve the
use of eDNA as a tool for tracking and monitoring marine mammal
distributions at meso- and macro-scales.

The postdoctoral scholar in this position will collaboratively develop
spatial models to describe the 3D distribution of target cetacean species
using eDNA. The position will entail a combination of spatial modeling,
genetic labwork, and bioinformatics. We seek a candidate with a strong
skill set in either spatial modeling or genetics/eDNA, and will provide
peer training to complement the skills the postdoc already has.

We are a collaborative team of researchers from the University of
Washington, NOAA, Scripps Institution of Oceanography, and St. Andrews. The
successful candidate will work closely with multiple collaborating labs at
UW, as well as with local researchers at the NOAA Northwest Fisheries
Science Center, to generate sequence data from eDNA samples and incorporate
those data into 3D spatial distribution models.

The term is 1.5 years, renewable subject to performance and available
funding; the larger MMARINeDNA project is funded for a five-year period.
For more information and to apply, please visit the following link:
https://apply.interfolio.com/111808

Interested candidates can also reach out to me directly [avanc...@uw.edu]
with any questions.

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D. 
(she/her/hers)

Assistant Professor
University of Washington | School of Aquatic and Fisheries Sciences
1122 NE Boat St
Seattle, WA 98105
Office: SAFS 216B
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[MARMAM] New publication: population trends in bottlenose dolphin stocks around the Hawaiian Islands

[Amy Van Cise]

Dear MARMAM,

On behalf of my co-authors, I'm happy to announce the publication of our
new paper, available at Endangered Species Research
:

Van Cise, AM, RW Baird, AE Harnish, JJ Currie, SH Stack, T Cullins, AM
Gorgone. 2021. Mark-recapture estimates reveal declines in abundance of
common bottlenose dolphin stocks in the main Hawaiian Islands. Endangered
Species Research 45:37-53. doi: https://doi.org/10.3354/esr01117


*Abstract*: Species conservation relies on understanding population
demographics, yet this information is lacking for many species and
populations. Four stocks of common bottlenose dolphins Tursiops truncatus
inhabiting the waters surrounding the main Hawaiian Islands (USA) are
exposed to anthropogenic disturbances including fisheries interactions,
tourism, naval activities, ocean noise, and contaminants. Although these
stocks are managed under the Marine Mammal Protection Act, a demographic
assessment has not been undertaken since 2006, and there is currently no
information on population trends. We combined regular survey effort with
citizen science contributions to estimate apparent survival and annual
abundance within each stock using photographs collected between 2000 and
2018. Over this time period, we collected 2818 high-quality identifications
of 765 distinctive individuals across all 4 stocks. Analyses of
inter-annual movements indicated that individuals exhibit restricted
habitat use within stocks, which contributed to non-random sampling. Annual
abundance estimates ranged from the 10s to the low 100s. Apparent survival
ranged from 0.84 to 0.9, with lower-than-expected estimates in all stocks.
Annual abundance estimates declined in 3 of the 4 stocks; however, this
decline was not significant for the Kaua‘i/Ni‘ihau and O‘ahu stocks, and
may be an artifact of sampling design in all stocks. Given the small
population size for these stocks, it is important to closely monitor trends
in abundance as a first step in mitigating negative effects of
anthropogenic activities. Future efforts should focus on consistent
geographic coverage in all stocks to decrease model uncertainty and improve
trend assessment.

The paper is open access and can be downloaded from ESR
, but please feel free
to reach out to me or my co-authors with any questions you may have.

Warm regards,
Amy

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D. 
(she/her/hers)

Research Associate, North Gulf Oceanic Society

Visiting Scientist, Genetics and Evolution Program

NOAA Northwest Fisheries Science Center
2725 Montlake Blvd E
Seattle, WA
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[MARMAM] CORRECTION: community survey on collaborative sample sharing

[Amy Van Cise]

***Please note that the original email used a link to an incorrect version
of this survey. The link has been corrected in the email that is below, and
can also be found here
<https://docs.google.com/forms/d/e/1FAIpQLSdhNckKcgfcWijZRLs6mJi0KMzPnTSp9xRMGKfvu8iBDsVeUA/viewform?gxids=7628>
.

Dear MARMAM community,

In an effort to estimate the frequency and extent of collaborative sample
sharing in marine mammal research, I and my colleagues have generated a
short (3-5 minute) survey
<https://docs.google.com/forms/d/e/1FAIpQLSdhNckKcgfcWijZRLs6mJi0KMzPnTSp9xRMGKfvu8iBDsVeUA/viewform?gxids=7628>
and
are hoping for responses from a representative sample of the marine mammal
research community. The survey comes in two sections: the first section
documents published studies that have involved sample sharing and is
intended for analysis to be included in an upcoming literature review of
best practices in sample collection, processing, and archival; the second
(optional) section assesses individual interest in sharing samples or data
for collaborative studies and is intended only to gauge community opinion
on this topic and the potential for future workshops or discussion of the
topic.

We appreciate your support in completing this survey
<https://docs.google.com/forms/d/e/1FAIpQLSdhNckKcgfcWijZRLs6mJi0KMzPnTSp9xRMGKfvu8iBDsVeUA/viewform?gxids=7628>.
Please complete the survey by *January 29, 2021*. Although response time
may vary, we expect it to take an average of *3-5 minutes* to complete both
sections of the survey.

survey url:
https://docs.google.com/forms/d/e/1FAIpQLSdhNckKcgfcWijZRLs6mJi0KMzPnTSp9xRMGKfvu8iBDsVeUA/viewform?gxids=7628

Thank you all for your help, and best wishes in 2021.

Sincerely,
Kim Parsons, Alix Switzer, and Amy Van Cise

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D. <https://amyvancise.weebly.com/>
(she/her/hers)

Research Associate, North Gulf Oceanic Society
<http://www.whalesalaska.org/>
Visiting Scientist, Genetics and Evolution Program
<https://www.fisheries.noaa.gov/west-coast/science-data/genetics-and-evolution-pacific-northwest>
NOAA Northwest Fisheries Science Center
2725 Montlake Blvd E
Seattle, WA
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[MARMAM] community survey on collaborative sample sharing

[Amy Van Cise]

Dear MARMAM community,

In an effort to estimate the frequency and extent of collaborative sample
sharing in marine mammal research, I and my colleagues have generated a
short (3-5 minute) survey
<https://docs.google.com/forms/d/1AZ83WLb6OZehrXUkf_IPytopcfgiCBE0eQ5Mo2egs2I/edit?usp=sharing>
and
are hoping for responses from a representative sample of the marine mammal
research community. The survey comes in two sections: the first section
documenting published studies that have involved sample sharing and is
intended for analysis to be included in an upcoming literature review of
best practices in sample collection, processing, and archival; the second
(optional) section assessing individual interest in sharing samples or data
for collaborative studies and is intended only to gauge community opinion
on this topic and the potential for future workshops or discussion of the
topic.

We appreciate your support in completing this survey
<https://docs.google.com/forms/d/1AZ83WLb6OZehrXUkf_IPytopcfgiCBE0eQ5Mo2egs2I/edit?usp=sharing>.
Please complete the survey by *January 29, 2021*. Although response time
may vary, we expect it to take an average of *3-5 minutes* to complete both
sections of the survey.

survey url:
https://docs.google.com/forms/d/1AZ83WLb6OZehrXUkf_IPytopcfgiCBE0eQ5Mo2egs2I/edit?usp=sharing

Thank you all for your help, and best wishes in 2021.

Sincerely,
Kim Parsons, Alix Switzer, and Amy Van Cise

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D. <https://amyvancise.weebly.com/>
(she/her/hers)

Research Associate, North Gulf Oceanic Society
<http://www.whalesalaska.org/>
Visiting Scientist, Genetics and Evolution Program
<https://www.fisheries.noaa.gov/west-coast/science-data/genetics-and-evolution-pacific-northwest>
NOAA Northwest Fisheries Science Center
2725 Montlake Blvd E
Seattle, WA
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[MARMAM] New publication: ecological and health-related dynamics of skin microbiomes on free-ranging beluga whales

[Amy Van Cise]

Hi MARMAM,

I and my co-authors are excited to announce a new paper on the dynamics of
beluga whale skin microbiomes, published in Animal Microbiome:

Van Cise, A. M., Wade, P. R., Goertz, C. E. C., Burek-Huntington, K.,
Parsons, K. M., Clauss, T., Hobbs, R.C., Apprill, A. (2020). Skin
microbiome of beluga whales: spatial, temporal, and health-related
dynamics. Animal Microbiome, 2(1), 39.
https://doi.org/10.1186/s42523-020-00057-1

The paper is open access, and can be downloaded here
 (shareable
link: https://rdcu.be/b8WI3). If you have any questions about the paper or
issues downloading, please don't hesitate to contact me (avanc...@gmail.com)
or Amy Apprill (aappr...@whoi.edu).

*Abstract*

*Background:* Host-specific microbiomes play an important role in
individual health and ecology; in marine mammals, epidermal microbiomes may
be a protective barrier between the host and its aqueous environment.
Understanding these epidermal-associated microbial communities, and their
ecological-or health-driven variability, is the first step toward
developing health indices for rapid assessment of individual or population
health. In Cook Inlet, Alaska, an endangered population of beluga
whales (*Delphinapterus
leucas*) numbers fewer than 300 animals and continues to decline, despite
more than a decade of conservation effort. Characterizing the epidermal
microbiome of this species could provide insight into the ecology and
health of this endangered population and allow the development of minimally
invasive health indicators based on tissue samples.

*Results:* We sequenced the hypervariable IV region of bacterial and
archaeal SSU rRNA genes from epidermal tissue samples collected from
endangered Cook Inlet beluga whales (n = 33) and the nearest neighboring
population in Bristol Bay (n = 39) between 2012 and 2018. We examined the
sequences using amplicon sequence variant (ASV)- based analyses, and no
ASVs were associated with all individuals, indicating a greater degree of
epidermal microbiome variability among beluga whales than in previously
studied cetacean species and suggesting the absence of a species-specific
core microbiome. Epidermal microbiome composition differed significantly
between populations and across sampling years. Comparing the microbiomes of
Bristol Bay individuals of known health status revealed 11 ASVs associated
with potential pathogens that differed in abundance between healthy
individuals and those with skin lesions or dermatitis. Molting and
non-molting individuals also differed significantly in microbial diversity
and the abundance of potential pathogen-associated ASVs, indicating the
importance of molting in maintaining skin health.

*Conclusions:* We provide novel insights into the dynamics of Alaskan
beluga whale epidermal microbial communities. A core epidermal microbiome
was not identified across all animals. We characterize microbial dynamics
related to population, sampling year and health state including level of
skin molting. The results of this study provide a basis for future work to
understand the role of the skin microbiome in beluga whale health and to
develop health indices for management of the endangered Cook Inlet beluga
whales, and cetaceans more broadly.


Warm regards,

Amy


<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D. 
(she/her/hers)

Research Associate, North Gulf Oceanic Society

Visiting Scientist, Genetics and Evolution Program

NOAA Northwest Fisheries Science Center
2725 Montlake Blvd E
Seattle, WA
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[MARMAM] New publication: evidence of link between marine mammal phylogeny and skin microbiota

[Amy Van Cise]

Dear MARMAM,

On behalf of my co-authors, I'm happy to announce the publication of our
new paper, available at RSOS
<https://royalsocietypublishing.org/doi/10.1098/rsos.192046>:

Apprill A, Miller C, Van Cise A, U’Ren JM, Leslie MS, Weber L, Baird RW,
Robbins J, Landry S, Niemeyer M, Rose K, Bogomolni A, Waring G. 2020.
Marine mammal skin microbiotas are influenced by host phylogeny. Royal
Society of Open Science. 7: 192046. doi.org/10.1098/rsos.192046

*Abstract*: Skin-associated microorganisms have been shown to play a role
in immune function and disease of humans, but are understudied in marine
mammals, a diverse animal group that serve as sentinels of ocean health. We
examined the microbiota associated with 75 epidermal samples
opportunistically collected from nine species within four marine mammal
families, including: Balaenopteridae (sei and fin whales), Phocidae
(harbour seal), Physeteridae (sperm whales) and Delphinidae (bottlenose
dolphins, pantropical spotted dolphins, rough-toothed dolphins,
short-finned pilot whales and melon-headed whales). The skin was sampled
from free-ranging animals in Hawai‘i (Pacific Ocean) and off the east coast
of the United States (Atlantic Ocean), and the composition of the bacterial
community was examined using the sequencing of partial small subunit (SSU)
ribosomal RNA genes. Skin microbiotas were significantly different among
host species and taxonomic families, and microbial community distance was
positively correlated with mitochondrial-based host genetic divergence. The
oceanic location could play a role in skin microbiota variation, but skin
from species sampled in both locations is necessary to determine this
influence. These data suggest that a phylosymbiotic relationship may exist
between microbiota and their marine mammal hosts, potentially providing
specific health and immune-related functions that contribute to the success
of these animals in diverse ocean ecosystems.

The paper is open access and can be downloaded from RSOS
<https://royalsocietypublishing.org/doi/10.1098/rsos.192046>, but please
feel free to reach out to myself or the primary author, Amy Apprill (
aappr...@whoi.edu), with any questions you may have.

Warm regards,
Amy Van Cise

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy M. Van Cise, Ph.D.
Research Biologist, Cascadia Research Collective
<http://www.cascadiaresearch.org/>
Guest Investigator, Woods Hole Oceanographic Institution
<https://www.whoi.edu/>

218 1/2 4th Ave W
Olympia, WA 98501
https://amyvancise.weebly.com/ <https://amyvancise.wordpress.com/>
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[MARMAM] New publication: phylogeography and taxonomy of two putative subspecies of short-finned pilot whale

[Amy Van Cise]

Dear MARMAM,

On behalf of my co-authors, I'm happy to announce the publication of our
new paper, available in early view
:

Van Cise, AM, RW Baird, CS Baker, S Cerchio, D Claridge, R Fielding, B
Hancock-Hanser, J Marrero, KK Martien,  AA Mignucci-Giannoni, EM Oleson, M
Oremus, MM Poole, PE Rosel, BL Taylor, PA Morin. 2019. Oceanographic
barriers, divergence, and admixture: Phylogeography and taxonomy of two
putative subspecies of short‐finned pilot whale. *Molecular Ecology *
https://doi.org/10./mec.15107.

*Abstract*: Genomic phylogeography plays an important role in describing
evolutionary processes and their geographic, ecological, or cultural
drivers. These drivers are often poorly understood in marine environments,
which have fewer obvious barriers to mixing than terrestrial environments.
Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty
in obtaining morphological data, can hamper our understanding of these
processes. One such taxon, the short‐finned pilot whale, is recognized as a
single global species but includes at least two distinct morphological
forms described from stranding and drive hunting in Japan, the “Naisa” and
“Shiho” forms. Using samples (n = 735) collected throughout their global
range, we examine phylogeographic patterns of divergence by comparing
mitogenomes and nuclear SNP loci. Our results suggest three types within
the species: an Atlantic Ocean type, a western/central Pacific and Indian
Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho)
type. mtDNA control region differentiation indicates these three types form
two subspecies, separated by the East Pacific Barrier: Shiho short‐finned
pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa
short‐finned pilot whale, throughout the remainder of the species'
distribution. Our data further indicate two diverging populations within
the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and
Indian Oceans, separated by the Benguela Barrier off South Africa. This
study reveals a process of divergence and speciation within a
globally‐distributed, mobile marine predator, and indicates the importance
of the East Pacific Barrier to this evolutionary process.

You can access the paper through early view
, or please
contact me if you need a pdf copy and don't have access to one.

Warm regards,
Amy

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><

Amy M. Van Cise, Ph.D.
Postdoctoral Scholar, Woods Hole Oceanographic Institution

Sensory Ecology and Bioacoustics Lab 
266 Woods Hole Rd
Marine Research Facility 236
MS#50
Woods Hole, MA, 02543

508-289-3419
https://amyvancise.weebly.com/ 
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[MARMAM] New paper: dialect differences among sympatric groups of pilot whales

[Amy Van Cise]

Dear MARMAM,

On behalf of my co-authors, I'm happy to share a new publication on vocal
dialect differences among sympatric groups of pilot whales in the Hawaiian
Islands:

Van Cise, A.M., Mahaffy, S.D., Baird, R.W., Mooney, T.A., Barlow J. (2018)
Song of my people: dialect differences among sympatric social groups of
short-finned pilot whales in Hawai’i. Behav Ecol Sociobiol 72: 193.
https://doi.org/10.1007/s00265-018-2596-1

Abstract:
In many social species, acoustic dialects are used to differentiate among
social groups within a local population. These acoustic dialects and their
corresponding social groups are often related to distinct foraging
behaviors or spatial movement patterns, and it is possible that vocal
repertoire variability is one of the proximate mechanisms driving or
maintaining genetic and ecological diversity at a subspecies level in
social species. Short-finned pilot whales (*Globicephala macrorynchus*)
inhabiting Hawaiian waters have a stable hierarchical social structure,
with familial social units associating in larger social clusters within
island-associated communities. In this study, we test the hypothesis that
sympatric social groups of short-finned pilot whales have acoustically
differentiated dialects, which may be used to maintain the social
structure. We first examined call composition of social calls collected
from photographically identified social clusters of short-finned pilot
whales around the Main Hawaiian Islands, using a catalog of manually
classified calls, and found that call composition differed among clusters.
We then conducted ANOVA and support vector machine (SVM) learning analyses
of the acoustic features of social calls. Social clusters were
significantly differentiated in their acoustic features, and the SVM
classification accuracy was 60%. These results indicate that vocal
repertoire reflects social segregation in short-finned pilot whales and may
be a driving mechanism of differentiation, potentially contributing to
genetic diversity within populations. This suggests divergent acoustic
population structure; however, the small sample size in this study
decreases the ability to detect acoustic differences among groups.
Additional sampling will improve our power to detect acoustic differences
among social clusters of Hawaiian pilot whales and improve classification
accuracy. The pattern described here highlights the importance of
increasing the spatial and temporal resolution of conservation and
management plans for this species, in order to conserve subpopulation
genetic and social structure.

The article can be accessed at
https://link.springer.com/article/10.1007/s00265-018-2596-1, or email me
directly for a pdf copy.

Best,
Amy

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><

Amy M. Van Cise, Ph.D.
Postdoctoral Scholar, Woods Hole Oceanographic Institution

Sensory Ecology and Bioacoustics Lab
266 Woods Hole Rd
Marine Research Facility 236
MS#50
Woods Hole, MA, 02543

508-289-3419
https://amyvancise.wordpress.com
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[MARMAM] New publication: relatedness and socio-genetic links in short-finned pilot whales

[Amy Van Cise]

Dear MARMAM community,

On behalf of my coauthors, I would like to announce a recent publication
examining links between social and genetic structure in the Hawaiian
population of short-finned pilot whales.

Van Cise, AM, KK Martien, SD Mahaffy, RW Baird, DL Webster, JH Fowler, EM
Oleson, PA Morin. 2017. *Familial social structure and socially-driven
genetic differentiation in Hawaiian short-finned pilot whales.* Molecular
Ecology 26(23): 6730-6741.

*Abstract:* Social structure can have a significant impact on divergence
and evolution within species, especially in the marine environment, which
has few environmental boundaries to dispersal. On the other hand, genetic
structure can affect social structure in many species, through an
individual preference towards associating with relatives. One social
species, the short-finned pilot whale (*Globicephala macrorhynchus*), has
been shown to live in stable social groups for periods of at least a
decade. Using mitochondrial control sequences from 242 individuals and
single nucleotide polymorphisms from 106 individuals, we examine population
structure among geographic and social groups of short-finned pilot whales
in the Hawaiian Islands, and test for links between social and genetic
structure. Our results show that there are at least two geographic
populations in the Hawaiian Islands: a Main Hawaiian Islands (MHI)
population and a Northwestern Hawaiian Islands/Pelagic population (*F*ST and
ΦST *p *< .001), as well as an eastern MHI community and a western MHI
community (*F*ST *p *= .009). We find genetically driven social structure,
or high relatedness among social units and clusters (*p *< .001), and a
positive relationship between relatedness and association between
individuals (*p *< .0001). Further, socially organized clusters are
genetically distinct, indicating that social structure drives genetic
divergence within the population, likely through restricted mate selection (
*F*ST *p *= .05). This genetic divergence among social groups can make the
species less resilient to anthropogenic or ecological disturbance.
Conservation of this species therefore depends on understanding links among
social structure, genetic structure and ecological variability within the
species.

The article can be accessed here:
http://onlinelibrary.wiley.com/doi/10./mec.14397/abstract

If you have issues accessing the article and would like a pdf copy, or have
any questions, you can contact me directly at avanc...@gmail.com.

Best wishes,
Amy Van Cise



<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><

Amy M. Van Cise, Ph.D.
https://amyvancise.wordpress.com

Scripps Institution of Oceanography
Ritter Hall 117
781-686-6753
avanc...@ucsd.edu

NOAA Southwest Fisheries Science Center
8901 La Jolla Shores Drive
858-546-5648
avanc...@gmail.com
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[MARMAM] New publication: Acoustic differentiation between two types of short-finned pilot whale in the Pacific Ocean

[Amy Van Cise]

Dear colleagues,

On behalf of my co-authors, I'm happy to announce the publication of the
following paper in the Journal of the Acoustical Society of America:

Van Cise AM, Roch MA, Baird RW, Aran Mooney T, Barlow J (2017) *Acoustic
differentiation of Shiho- and Naisa-type short-finned pilot whales in the
Pacific Ocean.* The Journal of the Acoustical Society of America, 141,
737–748. DOI: http://dx.doi.org/10.1121/1.4974858

Abstract
Divergence in acoustic signals used by different populations of marine
mammals can be caused by a variety of environmental, hereditary, or social
factors, and can indicate isolation between those populations. Two types of
genetically and morphologically distinct short-finned pilot whales, called
the Naisa- and Shiho-types when first described off Japan, have been
identified in the Pacific Ocean. Acoustic differentiation between these
types would support their designation as sub-species or species, and
improve the understanding of their distribution in areas where genetic
samples are difficult to obtain. Calls from two regions representing the
two types were analyzed using 24 recordings from Hawai‘i (Naisa-type) and
12 recordings from the eastern Pacific Ocean (Shiho-type). Calls from the
two types were significantly differentiated in median start frequency,
frequency range, and duration, and were significantly differentiated in the
cumulative distribution of start frequency, frequency range, and duration.
Gaussian mixture models were used to classify calls from the two different
regions with 74% accuracy, which was significantly greater than chance. The
results of these analyses indicate that the two types are acoustically
distinct, which supports the hypothesis that the two types may be separate
sub-species.

You can access this paper online at http://asa.scitation.org/
doi/abs/10.1121/1.4974858, or email me directly for a pdf copy.


Best regards,
Amy


<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><

Amy Van Cise
PhD Candidate
NSF Graduate Research Fellow
https://amyvancise.wordpress.com

Scripps Institution of Oceanography
Ritter Hall 117
781-686-6753 <(781)%20686-6753>
avanc...@ucsd.edu

NOAA Southwest Fisheries Science Center
8901 La Jolla Shores Drive
858-546-5648 <(858)%20546-5648>
avanc...@gmail.com
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[MARMAM] New publication: phylogeography of Pacific short-finned pilot whales

[Amy Van Cise]

Dear MARMAM colleagues,

On behalf of my coauthors I am pleased to share our recent publication on
the phylogeography of short-finned pilot whales in the Pacific Ocean,
published in the October 2016 edition of Marine Mammal Science:

Van Cise, AM, PA Morin, RW Baird, AR Lang, KM Robertson, SJ Chivers, RL
Brownell, KK Martien. 2016.* Redrawing the map: mtDNA provides new insight
into the distribution and diversity of short-finned pilot whales in the
Pacific Ocean.* Marine Mammal Science, 32(October), pp.1177–1199.

Abstract:
Correlations between morphological and genetic data provide evidence to
delineate species or evolutionarily significant units, which then become
the units to conserve in management plans. Here, we examine the
distribution and genetic differentiation of two morphotypes of short-finned
pilot whale (*Globicephala macrorhynchus*) in the Pacific Ocean.
Mitochondrial control region sequences from 333 samples were combined with
152 previously published sequences to describe genetic variability globally
and population structure in the Pacific. Although genetic variability is
low, we found strong differentiation at both broad and local levels across
the Pacific. Based on genetics, two types are distributed throughout the
Pacific, one predominantly in the eastern Pacific and the other in the
western and central Pacific. In the eastern Pacific Ocean, no correlation
was found between distribution and sea surface temperature. The two types
have broad latitudinal ranges, suggesting their distributions are likely
driven by more complex factors, such as prey distribution, rather than sea
surface temperature.

Full text and pdf can be downloaded here:
http://onlinelibrary.wiley.com/doi/10./mms.12315/abstract

Or to request a pdf directly, email me at avanc...@gmail.com

Best,
Amy Van Cise


<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><
Amy Van Cise
PhD Candidate
NSF Graduate Research Fellow
https://amyvancise.wordpress.com

Scripps Institution of Oceanography
Ritter Hall 117
781-686-6753
avanc...@ucsd.edu

NOAA Southwest Fisheries Science Center
8901 La Jolla Shores Drive
858-546-5648
avanc...@gmail.com
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[MARMAM] requesting short-finned pilot whale samples for taxonomic study

[Amy Van Cise]

Dear MARMAM,

NOAA's Southwest Fisheries Science Center has been working to complete a
global genetic analysis of short-finned pilot whale taxonomy, expanding on
data already generated primarily from the eastern and central Pacific, in
order to resolve several taxonomic questions about the species using
mitogenomes and nuclear SNPs. Our goal is to add approximately 150
mitogenomes and 100 nuclear samples to our current data set.

We have limited numbers of samples outside of the eastern Pacific, the
Hawaiian Islands and the Mariana Islands, so we are looking for additional
short-finned pilot whale samples from target areas. Priority areas for us
are:

Southern Hemisphere
Western Pacific
Indian Ocean
Eastern Atlantic

If anyone in the MARMAM community has samples they would be willing to
share, please contact us directly. In large studies like this we have many
sample contributors, so in order to be fair and keep authorship lists under
control, we typically offer co-authorship only when the number of samples
is a substantial portion of the total, though we make exceptions for
particularly important sample locations.

Thank you,
Amy Van Cise
Phil Morin
Karen Martien

<*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><  <*)))><

Amy Van Cise
PhD Candidate
https://amyvancise.wordpress.com

Scripps Institution of Oceanography
Ritter Hall 117
781-686-6753
avanc...@ucsd.edu

NOAA Southwest Fisheries Science Center
8901 La Jolla Shores Drive
858-546-5648
avanc...@gmail.com
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