Weisrock Lab Research

PI: David Weisrock
Postdoc: Megan Seifert

Postdoc: Kathryn M Everson, Added 03/02/2021
PhD Students: Paul Hime, Scott Hotaling, Justin Kratovil, Mason Murphy, Schyler Nunziata, Allison Sperling, Willian Licht, David Weisenbeck (Added on MCC resource 09/19/2023)
Undergraduate students: Jose Bocanegra, Mary Foley, Ricky Grewelle, Deborah Lu, Toluwalope Odukoya, Anna M Townsend


Lab Research Activities

Research in my lab involves the study of genetic variation among populations, species, and deeper evolutionary lineages. Within this broad range of research, we conduct a number of specific research projects. At the finest scale of population level questions, we aim to assess the impact that environmental change over recent time has had on genetic variation within populations, and how this variation is shared among populations. We extend these questions to the study of genetic variation at the population-species interface. Finally, we have interests

De Novo Genome Assembly

Study of de novo genome on two different insect species.

Personnel - UNIX Group

Wesirock, David PI
Hotaling, Scott
Nunziata, Schyler
Hime, Paul
Justin, Kratovil
Murphy, Mason
Foley, Mary
Grewelle, Richard
Lu, Deborah
Lawrence, Nicolette
Humphrey, Mackenzie
Mariah Donohue
Derek Filipek
Benjamin Browning
Hannah K Allen, Added on LCC resources on 04/29/2022 
Carlos Joaquin Pavon Vazquez, Post Doctoral Scholar, Added on LCC resources 06/17/2022

Software

Velvet
ABySS
GPUs

Species Delimitation and Phylogeny of North American Tiger Salamanders.

Description: Salamanders of the Ambystoma trigrinum complex represent have the largest geographic distribution of any North American amphibian radiation. Species boundaries and evolutionary relationships in this system have been poorly clarified. We are using next generation sequence data sampled from multiple populations across the range of the tiger salamander complex to perform species delimitation and species tree reconstruction for this system.

Personnel:

Paul Hime
Scott Hotaling
Schyler Nunziata
Kelly Lin Sovacool, UG
David Weisrock

Benjamin Browning

Computational Methods: DNA substitution model estimation, population structure analyses, species delimitation, gene tree reconstruction, species tree reconstruction

Software:

PAUP*, BPP, *BEAST, STEM-Hy, MrBayes, BUCKy, jModelTest, STRUCTURE, BAPS

Assembly of Whole-Genomic and Transcriptomic Next-Generation Sequence Data.

Description: Many of our studies are facilitated or improved through the generation of genomic assemblies for focal taxa. In an number of projects, these assemblies are used to develop markers that will be employed in subsequent phylogenetic studies (e.g., amplicon sequencing). IN other projects where population genomic data has been generated in a somewhat random fashion, assemblies are used to establish orthology and gene ontology. Most of our genome assembly work is performed in a de novo fashion, requiring large memory requirements and substantial computation time.

Personnel:

Paul Hime
Scott Hotaling
Schyler Nunziata
Justin Kratovil
Mason Murphy
David Weisrock

Computational Methods: data quality filtering, genome assembly

Software:

fastx_toolkit, ea-utils, jellyfish, Quake, SOAPdenovo2, FLASH, SNAP, BWA, Allpaths, BLAST2GO,

Population Genomic and Phylogenetic Analysis of Glacially-Tied, Imperiled Alpine Insects in the Pacific Northwest.

Description: Climate change is rapidly altering ecosystems worldwide and this warming is directly impacting species across taxonomic scales, from microbes to megafauna. Interestingly, warming is occurring most rapidly in high-elevation and latitudes areas of Earth and this warming is resulting in massive loss of permanent glacial and snowfield mass. For specialized, sensitive species residing in the meltwater of these meltwater masses, climate change represents a direct threat. And, when it comes to potential extinctions due to climate change, many reason that these meltwater inhabitants represent the biotic ‘canary in the coal mine’ of climate change. But, relatively is known of the extent of genetic variation and potential for adaptation among these organisms. For this project, we are focusing on a stonefly (Lednia tumana) and two caddisflies (Rhyacophila ebria and Allomyia bifosa) to address basic population genetic and demographic questions as well as identify populations (and the associated genomic variation within them) that may be better suited to adapting and persisting under future warming scenarios. This work will be carried out primarily in the Pacific Northwest with a central focus on Glacier National Park in Montana but it’s results hold wide application in mountain systems worldwide.

Personnel:

Scott Hotaling, David Weisrock

Computation Methods: data quality filtering, genome assembly, population genetic analysis

Software:

fastx_toolkit, ea-utils, jellyfish, Quake, SOAPdenovo2, FLASH, SNAP, BWA, Allpaths, BLAST2GO, Migrate, STRUCTURE, STACKS

PhD Student Group addition 11/08/2017

Thomas Maigret
I want Tom Maigret added to my lab group for DLX. Tom is a PhD student in Biology advised by Jim Krupa. I’m a committee member for Tom and he is performing all of his molecular work and population genetic analysis in my lab. Tom has had a DLX account (and I guess still has one), but until recently it was as part of Jeremiah’s bioinformatics class, and he no longer has access to the batch scheduler for his jobs.
Linkblue: tma244

David Weisrock
Department of Biology
University of Kentucky
dweis2@uky.edu
weisrocklab.com

Publications:

2013

1. Williams JS, Niedzwiecki JH, Weisrock DW. 2013. Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci. Molecular Phylogenetics and Evolution, 68:671-682.
2. O’Neill EM, Schwartz R, Bullock CT, Williams JS, Shaffer HB, Parra-Olea G, Aguilar-Miguel X, Weisrock DW. 2013. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma) species complex. Molecular Ecology, 22:111-129.

2012

1. Kajita Y, O’Neill EM, Zheng Y, Obrycki, Weisrock DW. 2012. A population genetic signature of human introduction efforts in an invasive lady beetle. Molecular Ecology, 21:5473-5483.

Funding: Project #1 has been funded through an NSF grant (2010-2014) with Weisrock serving as the lead PI.

Grants

Weisrock, David NO ID Paul Hime: Genome-scale resolution of species boundaries and demographyin Cryptobranchus Caribbean Wildlife Alliance 4/12/2013 - 12/31/2014 $1,000
Weisrock, David KSEF-148-502-13-315 KSEF RDE: Leveraging novel genetic and genomic technologies to understand and conserve a Kentucky state endangered giant salamander KY Science and Technology Co Inc 7/1/2013 - 6/30/2015 $30,000
Weisrock, David NO ID Nunziata: Microevolutionary response of two salamander species to climate change in an isolated seasonal wetland KY Academy of Science Foundation 3/7/2013 - 9/6/2014 $992
Weisrock, David NO ID Nunziata: Microevolutionary response of two salamander species to climate change in an isolated seasonal wetland Society for the Study of Amphibians and Reptiles 6/6/2013 - 7/31/2014 $500
Weisrock, David NO ID Scott Hotaling: Leveraging rad-sequencing to characterize recent divergence in an imperiled group of alpine invertebrates (Trichoptera: Rhyacophilidae) in Glacier National Park, Montana Society for the Study of Evolution 11/15/2013 - 11/14/2014 $2,250
Weisrock, David KSEF-148-502-13-315 KSEF RDE: Leveraging novel genetic and genomic technologies to understand and conserve a Kentucky state endangered giant salamander KY Science and Technology Co Inc 7/1/2013 - 6/30/2015 SCOPE
Weisrock, David DEB-1355000 Collaborative Research: Species tree reconstruction using neutral and non-neutral phylogenomic data. National Science Foundation 9/15/2014 - 8/31/2017 $597,224
Weisrock, David NO ID Paul Hime: Leveraging anchored hybrid enrichment to reveal genomic correlates of amphibian species richness. Society of Systematic Biologists 7/31/2013 - 7/30/2014 $2,000
Weisrock, David DEB-0949532 Genome level resolution of species boundaries and phylogeny of the north american tiger salamander radiation National Science Foundation 3/1/2010 - 2/28/2014 $450,000
Weisrock, David DEB-1406876 Doctoral Dissertation Research: Kratovil: Phylogeographic analysis of introgressive gene flow among nuclear loci functionally linked to the mitochondrion National Science Foundation 7/1/2014 - 6/30/2016 $19,485
Weisrock, David NO ID Dissertation Paul Hime: The Search for Sex-Linked Genes in Cryptobranchid Salamanders: Genome-Wide Gene Discovery and Marker Development Fresno Chaffee Zoo 12/1/2011 - 7/31/2014 $1,964
Weisrock, David NO ID Paul Hime: Leveraging genomics to understand and conserve the critically endangered Ozark hellbender salamander KY Academy of Science Foundation 2/12/2014 - 2/11/2015 $994
Weisrock, David NO ID Mason Murphy: Dispersal congruency and population structure within an imperiled host-parasite system KY Academy of Science Foundation 2/12/2014 - 2/11/2015 $933