Lab Meeting

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- Review Emily’s Paper

April 18-

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 Mtg- 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 Mtg

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