2022
Dec. 2022
From left to right top: Katie, Brandon, Remy, Annie, and Camille. From left to right bottom: Elisabeth and Madeline.
Lotterhos Lab Awards 2022:
"New Horizons Award" - Sarit for expanding her ecology research into genomics
"Lightbulb Award" - Camille for her review of adaptive capacity
"Save me from making a number of embarrassing mistakes award" - Brandon for finding mistakes in Katie L's code
"Award for managing people" - Remy for getting 12 people to help her process all her samples in one day
"Award for website design" - Annie for updating our protocols page with Quarto
"Award for data integrity" - Madeline for the seascape sample organization
"Award for most samples processed" - Elisabeth for being there to process every single oyster sample we collected!
Lotterhos Lab presentations
Brandon
Seminar to the NU-MSC
Annie
Undergraduate research symposium
Elisabeth
Undergraduate research symposium
Lab research featured in Quanta Magazine
Our lab's paper on supergene evolution was featured in Quanta Magazine's article on supergenes.
https://www.quantamagazine.org/how-supergenes-fuel-evolution-despite-harmful-mutations-20221108/
Nov. 2022
Lab Outreach with Beach Sisters
The Beach Sisters, students the Outreach Program's weekly afterschool program at Girls Inc of Lynn, visited the MSC last week to meet with Postdoc Remy Gatins, PhD Student Madeline Eppley, and Undergraduate Co-op Elisabeth Leung of the Lotterhos Lab. Students went on a lab tour and ID'd intertidal critters in the touch tanks.
The lab finished our oyster sampling for the year! Since May, we processed around 950 samples of the Eastern oyster between Texas and Canada. Over the winter we will continue to analyze these samples for genetics and disease. Here is a map of the spatial coverage put together by Madeline Eppley:
Oct. 2022
The lab continues to process samples of the Eastern oyster sent to us by collaborators from Texas to Canada. These samples will compromise the most comprehensive genetic survey ever completed for the species. It has been a huge effort!
Madeline, Elisabeth, and Annie process oysters
Annie samples tissues for genetic analysis
Sept. 2022
The Lab welcomes Camille Rumberger
Camille comes to us from UC Davis, where she worked on urchin population genetics.
Sampling oysters in the sun
Sampling oysters in the rain
August 2022
Lab photo before Sara Wagner headed off to university.
Remy Gatins processes Black Seas Bass for her range expansion study
Remy and her team processed over 100 samples in one day! These samples are being used in Remy's study of the health and fitness of black sea bass in their expanded range.
Juvenile black sea bass
Remy showing her team how to process fish
Sarah Wagner dissects a fish. Sarah is heading off to college at UMass Amherst, we'll miss her!
Lotterhos Lab welcomes Annie Christie
Co-op Annie Christie experiences the joys of oyster and fish processing on her first week. Annie Christie is a new intern in the lab through the Northeastern Co-Op program .
Lotterhos Lab attends the Evolving Seas Training and Integration Workshop at Shoals Marine Lab
We had a lot of fun at the Training and Integration Workshop, where RCN working groups presented results from their synthesis and training activities. https://rcn-ecs.github.io/2022-training/
Bottom right: Sarit Truskey (Hughes Lab), Katie Lotterhos, Madeline Eppley, Elisabeth Leung, and Camille Rumberger
Oyster sampling in Great Bay, NH
We continue to make progress toward our seascape genomics study of the entire range of the Eastern oyster. Last week we sampled Great Bay, NH with help from Brianna Group from the Nature Conservancy and Taja Sims-Harper from UNH. We used oyster tongs to sample the oysters from the boat. There was mud!
Elisabeth, Brianna, and Taja enjoying the nice weather
Top: Taja and Elisabeth tonging for oysters.
Bottom: Madeline, Katie, and Elisabeth
Madeline demonstrates proper oyster tong technique =)
July 2022
Our review on testing methods is published in Annual Reviews!
About the paper: Complex statistical methods are continuously developed across the fields of ecology, evolution, and systematics (EES). These fields, however, lack standardized principles for evaluating methods, which has led to high variability in the rigor with which methods are tested, a lack of clarity regarding their limitations, and the potential for misapplication. In this review, we illustrate the common pitfalls of method evaluations in EES, the advantages of testing methods with simulated data, and best practices for method evaluations. We highlight the difference between method evaluation and validation and review how simulations, when appropriately designed, can refine the domain in which a method can be reliably applied. We also discuss the strengths and limitations of different evaluation metrics. The potential for misapplication of methods would be greatly reduced if funding agencies, reviewers, and journals required principled method evaluation.
Read the paper: https://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-102320-093722
Get an overview from this twitter thread: https://twitter.com/DrK_Lo/status/1555157368916287488
Or watch this stop-motion animation about the paper!
Model Validation Program Update
We take a trip to the Virginia Institute of Marine Science! We are collaborating with Jess Small, Director of the Aquaculture Genetics & Breeding Technology Center, to test if oyster genotypes can predict their fitness in the field. The goal of our trip was to test non-invasive methods of genotyping small oysters (<55mm). To get into the oyster, we collected different tissues from notched oysters and relaxed oysters, and stored them in different ways. This data will help us make decisions about how to genotype and track the fitness of oysters in the field.
Hemolymph extraction
Katie and Madeline
Relaxed oysters
Note how they are gaping
Fun times in the lab
Madeline and Elisabeth take over the camera
June 2022
Lotterhos Lab attends Evolution 2022
Lotterhos Lab in Cleveland
From left: Madeline Eppley, Remy Gatins, Katie Lotterhos, and mentee Andy Lee (graduate student at Purdue)
Madeline's first poster
Madeline gives her first poster at a scientific conference (no thanks to the pandemic!)
Katie's 2022 Evolution Talk
"Re-examining the paradigm of genotype-environment associations: the paradox of adaptive phenotypic clines without clines in the underlying allele frequencies"
Katie Lotterhos and Brandon Lind attend a workshop with Eelgrass biologists discussing assisted gene flow.
An interesting discussion in this workshop was whether restoration projects should just transplant every possible genotype and let evolution and natural selection do the work. Although appealing, there are potential downsides to this idea, in that the majority of transplants could die and this could make funding agencies reluctant to fund further restoration efforts. It's ideal to use genetically appropriate stock based on sound rationale, as the best information is obtained if a majority of the genotypes live and a subset of them die.
May 2022 in the States
Oysters at VIMS
Graduate student Madeline Eppley and undergraduate co-op Elisabeth Leung visit our collaborator Jessica Small at the Virginia Institute of Marine Science (VIMS), where they received training in oyster aquaculture.
York River High Salinity Site
Oyster tables sit in the water just below the surface. Aquaculture oysters remain in bags on top of the tables. The pump house for the new Acuff Hatchery is at the end of the pier!
Lewisetta Low Salinity Site
This low salinity site hosts 4N tetraploid oysters.
May 2022 in Sweden
As part of her Fulbright exchange, Dr. Lotterhos is learning some new study systems in the Baltic Sea, including Zostera eelgrass. Here are some pictures of us snorkeling while we collect eelgrass near Tjärnö.
Marlene Jahnke
collecting eelgrass for genetics
Marlene and Jacob
separating shoots in the bags
Katie Lotterhos
snorkeling to collect
April 2022
As part of her Fulbright exchange, Dr. Lotterhos is learning some new study systems in the Baltic Sea, including Idotea isopods. Here are some pictures of isopods we collected near Tjärnö.
Idotea granulosa
Male vs. Female
Female is more pear-shaped
Idotea granulosa
brooding female, note the brown clumps of eggs inside the carapace
I. baltica vs. I. granulosa
comparison of two species, distinguished by the tail
Isopods play an important role in the ecosystem, because they eat epiphytes and other fouling organisms that grow on foundational species like eelgrass and Fucus seaweeds. Eelgrass and seaweeds are foundational species because provide structured habitat for the juveniles of many species, as shown below for Fucus. Isopods help to keep fouling organisms from choking out the eelgrass or seaweed. The water is cold, so we wear survival suits to help us stay warm.
3-spine stickeback
juvenile urchin
juvenile lumpsucker
survival suits
Uppsala Day
Dr. Lotterhos attends "Uppsala Day" as a Fulbright Scholar in Sweden.
March 2022
Our paper "Novel and disappearing climates in the global surface ocean from 1800 to 2100" is in the Top 100 Downloaded ecology Scientific Reports papers in 2021! The article received 6,224 article downloads in 2021, placing it in the top 100 out of almost 2,000 papers published.
March 2022
Remy and Madeline visit Dr. Lotterhos at Tjärnö. While they were here, we collected samples of representative species from the area for the Ocean Genome Legacy at Northeastern's Marine Science Center. These samples will be preserved and be made available to the research community around the world for study.
Madeline and Remy collecting samples
Madeline sorting species
Katie, Madeline, Remy on the dock
Tjärnö Kickoff highlights the international community that work here.
Dr. Lotterhos gives a Plenary Session at the European Society for Evolutionary Biology Working Group on Inversions at Tjärnö.
This conference brought together evolutionary biologists who work on inversions: areas of the genome that get flipped around. This flipping has important consequences for how organisms evolve and adapt to their environments, and can influence many traits!
Feb. 2022
Our paper Seeing the forest for the trees: Assessing genetic offset predictions from gradient forest is published in Evolutionary Applications.
This is the first study to rigorously evaluate a machine learning algorithm that has been used to predict fitness in response to climate change. We show that well it can perform well under some conditions, it can be biased by the population dynamics of the species and should be used with caution until it's behavior is better understood.
