Lab Meeting

Fall 2024

11/18/2024 Perciavalle and Opferman- Delving deeper: MCL-1's contributions to normal and cancer biology https://www.cell.com/trends/cell-biology/abstract/S0962-8924(12)00163-8
11/11/2024 Opferman Paper- Obligate Role of Anti-Apoptotic MCL-1 in the Survival of Hematopoietic Stem Cells https://www.science.org/doi/full/10.1126/science.1106114
11/04/2024 Opferman and Kothari- Anti-apoptotic BCL-2 family members in development https://www.nature.com/articles/cdd2017170
10/28/2024 Miles et al 2021- Urban evolution comes into its own: Emerging themes and future directions of a burgeoning field https://onlinelibrary.wiley.com/doi/full/10.1111/eva.13165
10/21/2024 No Lab Meeting
10/14/2024 No Lab Meeting- Fall Break
10/07/2024 Carlen et al 2021- Urbanization predicts flight initiation distance in feral pigeons (Columba livia) across New York City https://www.sciencedirect.com/science/article/abs/pii/S0003347221002013
09/30/2024 Matthew Practice Talk (plan on 2hr lab mtg)
09/23/2024 Williams et al 2024- Of Rarity and Symbolism: Understanding Human Perceptions of Charismatic Color Morphs https://link.springer.com/article/10.1007/s10745-024-00492-7
09/16/2024 No Lab Meeting- Emily to IBA
09/09/2024 Freezer Organization
09/02/2024 No Lab Meeting- Labor Day
08/26/2024 Emily IBA Practice Talk

Summer 2024

08/20/2024 Summer Goals Review and Fall Goals Setting
08/13/2024 NextFlow (But Emily giving talk at Arkansas State)
08/06/2024 NextFlow
07/23/2024 Group- Github to Nextflow set-up and usage
07/16/2024 Group- Github to HPC syncing; Github to Nextflow set-up
07/09/2024 Group- Github to HPC syncing session
07/02/2024 No Lab Meeting- Emily Vacation
06/25/2024 Summer Celebration
06/18/2024 No Lab Meeting- Emily and Heather to Meeting
06/11/2024 Brian- Nextflow

Spring 2024

06/04/2024 Kardos and Waples 2024- Low-coverage sequencing and Wahlund effect severely bias estimates of inbreeding, heterozygosity and effective population size in North American wolves (https://onlinelibrary.wiley.com/doi/full/10.1111/mec.17415)
05/28/2024 CV style discussion
05/21/2024 Summer 2024 Lab Goals
05/03/2024
04/26/2024 No Meeting- Exams
04/19/2024 Delaney- semester project update
04/12/2024 Alexandria and Brian- semester project updates
04/05/2024
03/29/2024 Work on BigBlue Migration / Free Day
03/22/2024 Matthew- Student Seminar Practice + Present New Data
03/15/2024 Meeting with HPC administrators
03/08/2024 Heather- Student Seminar Practice + Present New Data
03/01/2024 Phil- Thesis Practice Talk
02/23/2024 Attend CBio
02/16/2024 Big Blue migration planning
02/09/2024 Big Blue migration planning
02/02/2024 Emily- Prelim data presentation (eastern pop structure and demography) and discussion about future directions
01/26/2024 Alexandria- Poster Practice (and Semester Goal Planning, time permitting) / CBio
01/19/2024 Emily - State of the Lab

Fall 2023

Aug 29 No meeting first week of classes
Sept 5 Muthupalani et al 2014- GM1-gangliosidosis in American black  bears: Clinical, pathological, biochemical and molecular genetic  characterization
Sept 12 No Lab Meeting- Emily to UF to give seminar
Sept 19 Forester et al 2018- Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations
Sept 26 (Grads only)- Lab policies discussion
Oct 3 Hoban et al 2020- Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved
Oct 10 Hoban et al 2023- Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: An ongoing assessment of genetic indicators in nine countries
Oct 17 Alexandria Practice Talk (Fall Break)
Oct 24 Capblancq and Forester 2021- Redundancy analysis: A Swiss Army Knife for landscape genomics
Oct 31 Iacobucci and Mullighan 2017- Genetic Basis of Acute Lymphoblastic Leukemia
Nov 7 Alexandria Practice Talk- Round 2
Nov 14 Alvarado et al 2022- Genotype–environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence
Nov 21 Ahrens et al 2021- Regarding the F-word: The effects of data filtering on inferred genotype-environment associations
Nov 28 Maier et al 2022- Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad (Anaxyrus canorus)
December 5 Lauren and Brian present semester research projects

Summer 2023

May 23 Summer Goal Setting
(Wed) July 5 Phil Practice Talk- Mammalogy 
July 11 Wootton et al- Genomic health is dependent on long-term population demographic history
July 25 Emily Practice Talk- Tenure
Aug 1 Group outing- Barbie movie
Aug 8 Website updating (write blurbs, links, headshots)
Aug 22 Fall goals setting

Spring 2023

Jan 17 Semester Goals + Chores
Jan 24 Kaelin et al- bioRxiv- Ancestry dynamics and trait selection in a designer cat breed
Jan 31 Nietlisbach et al 2017- Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population
Feb 7 Matthew Practice Talk
Feb 14 Phil Practice Talk
Feb 21 Lab Goals Check-in; de Jong et al 2023- Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence
Feb 28 Zhuang et al 2019- Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids
Mar 7 Spring Break- Heather's Practice talk (optional)
Mar 14 Heather's Practice talk
Mar 21 Grundler and Rabosky 2021- Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction
Mar 28 Poster practice talks for Student Research Forum
April 4 Singhal et al 2022- No link between population isolation and speciation rate in squamate reptiles
April 11 No Lab Meeting
April 18 Review figures from Emily's paper
April 25 Grads write prospectus on-boarding document (Emily at EBBW)
May 2 No Lab Meeting- Grading
May 9 No Lab Meeting- Grading + Emily to HudsonAlpha to give Seminar

Fall 2022

Aug 24 No Lab Meeting- Adjust to Fall Semester
Aug 31 Semester Goals + Lab Chores + Brian HPC org
Sept 7 Partha et al 2017- Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling
Sept 14 No Lab Mtg- Emily out of town
Sept 21 No Lab Mtg- Emily Conservation Class Field Trip
Sept 28 Kingsley et al 2017- The ultimate and proximate mechanisms driving the evolution of long tails in forest deer mice
Oct 5 Phil- Prospectus Talk Practice
Oct 12 Hager et al 2022- A chr inversion contributes to divergence in multiple traits between deer mouse ecotypes
Oct 19 Kingsley et al 2018- Identity and novelty in the avian syrinx
Oct 26 Langbien et al 2010- The Keratins of the Human Beard Hair Medulla: The Riddle in the Middle
Nov 2 No Lab Meeting
Nov 9 Kiso et al 2009- The disruption of Sox21-mediated hair shaft cuticle differentiation causes cyclic alopecia in mice
Nov 16 Brian and Alexandria Present Results
Nov 23 No Lab Meeting- Thanksgiving 
Nov 30 Kowalczyk et al 2022- Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness
Dec 7 No Lab Meeting- Grading
Dec 14 Linoleum carving, stamping, glitter extravaganza  

Summer 2022

May 9 Summer Goal Planning and Scheduling with the Nudelman Lab
May 16 No paper; organizing mtg
May 23 & 30 No Lab Meeting
June 6 Evolution Practice Posters and Talks (block 2 hours)
June 13 Evolution Practice Poster Pollard; Practice Talk Puckett
July 11 Lab/Conference Finances Chat
July 26 Karczewski et al 2020- The mutational constraint spectrum quantified from variation in 141,456 humans WITH supplemental
Aug 9 Cole et al 2022- Genomic insights into the secondary aquatic transition of penguins

Spring 2022

Jan 13 SMART Goal Planning Session
Jan 31 Discussion of grant writing.  Read this grant.  Review this presentation.
Feb 7 Tam et al 2019.  Benefits and limitations of genome-wide association studies.
Feb 14 Phil Prospectus Practice Talk
Feb 21 Rahman et al 2021- A combined RAD-seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee.
Feb 28 Puckett et al pre-preprint
March 7 No Meeting- Spring Break
March 14 Isis and Caleigh Practice Posters
March 21 Matthew Practice Talk.  Everyone also plan to attend Undergraduate Research Forum today to support Isis and Caleigh.
March 28 DeCandia et al 2021. Sarcoptic mange severity is associated with reduced genomic variation and evidence of selection in Yellowstone National Park wolves.
April 4 Taron et al 2021.  A sliver of the past: The decimation of the genetic diversity of the Mexican wolf.
April 11 Heather Prospectus Practice Talk
April 18 Emily Practice Talk

Fall 2021

Aug 24 Introductions and Lab Policies
Aug 31 Semester Goals 
Sept 7 Puckett Practice Talk (Rat Phylogeography)
Sept 14 Lou et al 2021- A beginner’s guide to low-coverage whole genome sequencing for population genomics
Sept 21 Manel et al 2003- Landscape genetics: combining landscape ecology and population genetics
Sept 28 McRae 2006- Isolation by resistance
Oct 5 No Lab Meeting
Oct 12 No Lab Meeting- Fall Break
Oct 19 Cahill et al 2015- Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears
Oct 26 Choe and Jarvis 2020- The role of sex chromosomes and sex hormones in vocal learning systems
Nov 2 Wentzloff- Github Brown Bag
Nov 9 No Lab Meeting
Nov 16 Sexton et al 2014- Genetic isolation by environment or distance: which pattern of gene flow is most common?
Nov 23 Ruiz-Lopez et al 2016- A novel landscape genetic approach demonstrates the effects of human disturbance on the Udzungwa red colobus monkey (Procolobus gordonorum)
Nov 30 Davis- New Results Presentation

Summer 2021

May 5 Armstrong et al.  Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection
May 19 Evolution Practice Talks
June 30 Summer goal setting
July 7 Shultz and Sackton 2019. Immune genes are hotspots of shared positive selection across birds and mammals
July 14 Cingolani et al 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff
July 21 Louca and Pennell 2020. Extant timetrees are consistent with a myriad of diversification histories
July 28 Pollard- Draft manuscript review

Spring 2021

Jan 13 Rashid et al- From dinosaurs to birds: a tail of evolution
Jan 20 Jaramillo-Correa et al. Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse
Jan 27 Kyriazis et al. Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression
Feb 3 Ralls et al. Genetic rescue: A critique of the evidence supports maximizing genetic diversity rather than minimizing the introduction of putatively harmful genetic variation
Feb 10 Project updates
Feb 17 Weise et al. Adaptive genetic management: assessing the benefits of translocations
Feb 24 Fry et al. Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth
March 3 No meeting
March 10 Mooney et al. The impact of identity-by-descent on fitness and disease in natural and domesticated Canid populations
March 17 Project Updates
March 24 Upham et al. Ecological causes of uneven speciation and species richness in mammals
March 31 Pollard Practice Talk
April 7 No Lab Meeting- Wellness Break
April 14 Pollard Practice Talk
April 21 Murray et al. Natural selection shaped the rise and fall of passenger pigeon genomic diversity WITH supplemental
April 28 No Lab Meeting- Grading

Fall 2020

Aug 20 Kennedy et al. Taxonomic Assessment of the Black Bear (Ursus americanus) in the Eastern United States.
Aug 27 Lab Member Presentations: What I did this summer/Semester Goals
Sept 3 Edwards et al. Home range size variation in female Arctic grizzly bears relative to reproductive status and resource availability
Sept 10 Edwards et al. Fast carnivores and slow herbivores: differential foraging strategies among grizzly bears in the Canadian Arctic
Sept 17 Clendenin Elevator Pitch Practice; Cassin-Sackett et al. Do pathogens reduce genetic diversity of their hosts? Variable effects of sylvatic plague in black‐tailed prairie dogs
Sept 24 Pollard Elevator Pitch Practice; Tsuchiya et al. First Genome Sequence of the Gunnison’s Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague
Oct 1 Cassin-Sackett et al. Evidence for two subspecies of Gunnison’s prairie dogs (Cynomys gunnisoni), and the general importance of the subspecies concept
Oct 8 Clendenin and Pollard Practice Talks
Oct 15 No Meeting- Hosting Seminar
Oct 22 No Meeting- Hosting Seminar
Oct 29 Clendenin Practice Talk and Project Updates
Nov 5 Slatkin- Linkage disequilibrium- Understanding the evolutionary past and mapping the medical future
Nov 12 Meeting with Seminar Speaker
Nov 19 No Meeting- Exams and Grading
Nov 26 No Meeting- Thanksgiving
Dec 7 Special mtg with Daigle Lab: A translational model for venous thromoboembolism: microRNA expression in hibernating black bears

Summer 2020

May 28 McLellan and Reiner. A review of bear evolution.
June 4 Lariviere. Ursus americanus.
June 11 Pasitschniak-Arts. Ursus arctos.
June 18 No Meeting
June 25 DeMaster and Stirling. Ursus maritimus.
July 2 Beston. Variation in life history and demography of the American black bear.
July 9 Steyaert et al. The mating system of the brown bear Ursus arctos.
July 16 Mesa-Cruz et al. Litter size and cub age influence weight gain and development in American black bears
July 23 Fowler et al. Ecological plasticity of denning chronology by American black bears and brown bears. AND Rode et al. Den phenology and reproductive success of polar bears in a changing climate.
July 30 No Meeting
Aug 6 Kennedy et al. Variation in the Black Bear (Ursus americanus) in the Eastern United States and Canada.
Aug 13 Morphometrics Week- No Lab Meeting

Spring 2020

Jan 8 Conference Call
Jan 30 Rinker et al. Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift
Feb 5 Conference Call
Feb 11 Chen et al. Allele frequency dynamics in a pedigreed natural population
Feb 18 Project Updates
Feb 25 No Meeting
March 3 Card et al. Genomic Basis of Convergent Island Phenotypes in Boa Constrictors
March 10 No Meeting- Spring Break
March 17 Andrews et al. Harnessing the power of RADseq for ecological and evolutionary genomics
March 24 Unpublished preprint
March 31 Ceballos et al. Runs of homozygosity: Windows into population history and trait architecture
April 7 Pemberton et al. Genomic patterns of homozygosity in worldwide human populations
April 14 No Meeting
April 21 Szpiech et al.  Long runs of homozygosity are enriched for deleterious variation.
April 28 Benazzo et al. Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers (with supplemental)

Fall 2019

Aug 28 Conference Call
Sept 4 Balisi et al- Dietary specialization is linked to reduced species durations in North American fossil canids
Sept 11 Pappa et al- The bear necessities: A new dental microwear database for the interpretation of palaeodiet in fossil Ursidae
Sept 18 Pollard Practice Talk & Conference Call
Sept 25 No Meeting- International Sun Bear Symposium
Oct 2 No Meeting
Oct 9 Figueirido et al- Ecomorphological correlates of craniodental variation in bears and paleobiological implications for extinct taxa: an approach based on geometric morphometrics
Oct 16 Tarquini et al- Evolution of the Carnassial in Living Mammalian Carnivores: Diet, Phylogeny, and Allometry & Conference Call
Oct 23 Feigin et al- Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
Oct 30 Tollis et al- Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards
Nov 6 Tollis et al- Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)
Nov 13 Project Updates
Nov 20 Project Updates
Nov 27 No Meeting- Thanksgiving
Dec 4 Conference Call

Spring 2019

Jan 23 Kierepka and Latch- High gene flow in the American badger overrides habitat preferences and limits broadscale genetic structure
Jan 30 Kim et al- Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly
Feb 6 Giglio et al- Pedigree‐based genetic management improves bison conservation
Feb 13 Thybert et al- Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
Feb 20 Young et al- Conserved transcriptomic profiles underpin monogamy across vertebrates
Feb 27 Baurens et al-Recombination and Large Structural Variations Shape Interspecific Edible Bananas Genomes
March 6 No Meeting- Spring Break
March 13 Hu et al- Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas
March 20 Kaelin and Barsh-Genetics of Pigmentation in Dogs and Cats
March 27 Mallarino et al- Developmental mechanisms of stripe patterns in rodents
April 3 No Meeting- Association of Southeastern Biologists Meeting
April 10 Imsland et al- Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses
April 17 Pimiento et al- Evolutionary pathways toward gigantism in sharks and rays
April 24 No Meeting- Eastern Black Bear Workshop
May 1 Mitterboeck et al- Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes