News from the Lab

Bill elected to the National Academy of Sciences

Dr. William Murphy, the James E. Womack University Professor of Genetics at the VMBS, is one of 144 new members of the National Academy of Sciences. And we are one very proud lab group! Time to celebrate!

2 for 1 Canid Genomes

By combining F1 hybrids and trio-binning approaches we’ve been able to build ultra-continuous genomes for the Wolf and Coyote. All from an F1 Woyote. Check out the article in the Journal of Heredity to see how we did it.

KBTX Famous!

Nicole from the Murphy Lab stopped by the Focus at Four show to talk to Alex from KBTXNews about what swarming behavior in bats can teach us about bat immunity. Missed it – check out the video here

Darwin Day 2024

Darwin Day 2024 was an incredible success with 42 booths and over 1400 visitors taking over the Leach Teaching Gardens for an evening of evolutionary discovery. The Murphy Lab was out in force and posing the question “what do you get if you cross a Lion and a Tiger?”. Our booth explored amusingly named mammalian hybrids, invited people to draw their own hybrids, and explored the big question – what really makes a species a species?

Out now in Cell Genomics!

Check out our latest publication, which appeared in the February edition of Cell Genomics. The paper describes the phylogenomic history of the Old World Myotis bats. Our analyses suggest that the huge degree of introgression we see among divergent species maybe be due to their use of swarming behavior. During swarming multi-species, male-biased populations come together for mating. Our analysis suggests that swarming behaviour contributes to the exchange of immune variants amongst closely related species – a previously unexplored avenue to their exceptional immunity. Please also check out the excellent companion piece discussing the wider implications of our paper by Zhilong Yang and Guogie Zhang.

Out now in (and on the cover of) Nature Genetics!

Check out our latest publication, out now in the November issue of Nature Genetics. The paper describes the evolution of structural variation in cats as revealed by SINGLE-HAPLOTYPE (you read that right!) comparative genomics. Have a read and find out more about our “two-fer” trio-binning approach, how olfactory gene expansions have contributed to niche adaptation in fishing cats and much much more.

Holiday Party Season 2023

Holiday Party Season 2023 was a BBQ bonanza for the Lab. Starting with pulled pork Chez Foley. Then progressing to ribs and brisket and rounded out with a delightful Peach Cobbler at our joint lab party long with the Dindot, Criscitiello, Porter and Threadgill Labs. Word on science street is that the Murphy Lab was well represented at karaoke at the Biology Dept. Christmas Party aswell…

Aggie Research Program 2023

Suddenly, Summer was over and it was term-time again. Hao, Arjun, Emily and Sid joined Zoya and Julia this year on our undergraduate ARP research team. This semester, the team set out to understand what happens when deletions occur in ultra-conserved regions of mammalian genomes. The team will use a bioinformatic approach to determine if these zoonomia conserved deletions (zooConDels) result in phenotypic differences among clades of mammals.

Introducing PhD Student Jim Neugebauer

Jim Neugebauer joined the Murphy lab this year. He is co-supervised by Dr. Michael Tewes at Texas A&M University Kingsville at the Caeser Kleberg Wildlife Research Institute. He previously studied bobcats and black bears in Pennsylvania through both field and laboratory-based methods. Currently, he is studying genetic factors limiting conservation success in endangered ocelot populations in south Texas. When not working, Jim enjoys hunting with his dog Bleu, running, and saltwater fishing.

SMBE, Ferrara, Italy 2023

At the end of July, it was time to say ciao to the relentless Texas heat and say a big relieved buongiorno to the gentle Mediterranean climes of Italy. When we arrived in Ferrara, it was clear this meteorological fantasy was not to be… Local temperatures were around 42C/107F most days. While these temperatures are usually made bearable in Texas by pervasive frosty air conditioning, our novel urban diffused meeting in Ferarra was not. Undaunted, and armed with the hottest conference accessory, the SMBE opera fan, we wove our way around the narrow streets of Ferrara to various conference venues scattered throughout the city. The pinnacle of the venues was the Teatro Comunale di Ferrara which hosted the plenaries, various symposia and Bill’s invited talk on haploid cat comparative genomics. Countless gelato and aperitivo were consumed. For our health of course… To combat the heat… obviously…

EVOLUTION, Albuquerque, NM 2023

The annual Evolution Meeting in ABQ played host to a Murphy Lab Extravaganza featuring two talks and three posters discussing cats, bats, recombination, aardvarks, Phylogenomics and the Y-chromosome. Long days spent listening to so many must-see talks delightfully accompanied by some visits to local breweries.

We also had an unlikely meetup with two chemists trying to make their way into the Evolutionary Biology field. Good luck to them!

Bandelier National Monument, June 2023

We emerged from our retreat refreshed and ready for more science. So we jumped in our enormous Chevy Suburban and headed South to Albuquerque. On the way, we stopped by the Bandelier National Monument, for a hike and to check out how the Pueblo people lived along the cliffs and mesa’s many many years ago. A trip to Los Alamos was considered, made timely by the forthcoming Oppenheimer movies, but alas the lure and promise of more of Cafe Pasqual’s tacos, chile rellenos and salsas was too much.

Lab Retreat to Santa Fe, New Mexico, June 2023

In June this year, we packed our bags, laptops and pipettes and decamped to the mountains of New Mexico. It was a glorious escape from the Texas Summer and a chance to get down to some serious retreating.

We spent 3 days surrounded by the amazing local art, pondered the big science picture, ate enormous quantities of tacos “Christmas” style and plotting the next stages of our projects. We found some time learning to identify mammal tracks, write some lightning fast abstracts, participate in a “pro-tips knowledge exchange” and a bit of time every morning to engage in some heretical (for a mammal lab) birding.

Hot Off The Press!

We’re delighted to share our new paper detailing an updated genomic timescale for placental mammals that was released today as part of a special issue in Science celebrating the work of the Zoonomia Consortium

In the same issue be sure to check out our contributions to one of the Flagship papers which provides an overview of how the Zoonomia Project has enhanced our evolutionary understanding of mammals. This overview paper is also accompanied by a nice perspective piece

Murphy Lab Undergraduate Researchers Spring 2023 Semester – Team Recombination

Undergraduate Researchers Spring 2023

This semester Richie, Zoya, Srushti and Julia were joined by new team member Christian in their quest to generate recombination maps for diverse mammalian species. This year, Team Recombination added a Babboon, Sloth and Lion to our growing menagerie of mammalian recombination maps. We’ve also “spread our wings” a little outside of mammals and added maps for Darwin’s Finches and a Falcon.

11th International Conference on Canine & Feline Genetics & Genomics

A collage of Andrew, Bill and the cover of the 11th Annual ICCFGG in Alabama

This past October, Bill and Andrew presented at the 11th International Conference on Canine & Feline Genetics & Genomics (ICCFGG) in Huntsville, Alabama. Hosted every two years, ICCFGG provides a platform for researchers and clinicians from all over the world to share the latest advancements in canine and feline genetic and genomic research.

Andrew gave a presentation titled “Ultracontinuous genomes elucidate complex speciation patterns within Panthera,” describing how recent advancements in genome assembly and long-read sequencing enable a high-resolution look into the evolutionary histories woven throughout the genomes of big cats for which he received the outstanding student oral presentation award.

Team Panthera—Spring 2023 Undergraduate Researchers

Andrew and Undergraduate Researchers Spring 2023

The field of phylogenomics is rapidly advancing, and the ability to assess species-level relationships at a genome-wide scale is becoming readily available. Recent discoveries in phylogenomics have shown how hybridization between closely related species confounds standard phylogenetic approaches. To identify the true species relationship, one must evaluate both phylogenetic and genomic data types at a genome-wide scale.

Our project focuses on conducting whole genome phylogenomic analyses on each of the eight major cat lineages to understand better the distribution of evolutionary histories woven throughout the genomes of the various cat species through rampant hybridization and selection over the past 15 million years. Using state-of-the-art software and novel techniques, we will also identify true species relationships by comparing phylogenetic and genomic data types in addition to identifying genes under selection for specific traits/phenotypes.

Team: Megan Yang, Trevor Martinez, Ramya Bathala, William Cameron Walker, & Thanh-Thao Buu Ho

Team Recombination—Fall 2022 Undergraduate Researchers

Aggie Research Program Undergraduate Researchers in the Murphy Lab in Fall 2022This semester has seen Srushti and Julia join forces with returning Team Recombination members Richie and Zoya in their quest to generate recombination maps for diverse mammalian species, including a dolphin, a cow, an Asian leopard cat, a wolf, and a polar bear.

New Preprint

Check out our new preprint on bioRxiv.

5th Annual Southeast Texas Evolutionary Genetics & Genomics

STEGG logoThis June 3rd, the University of Houston’s Department of Biology and Biochemistry hosted
the 5th Annual Southeast Texas Evolutionary Genetics and Genomics (STEGG) conference.
This event brought together over 100 faculty, postdoctoral fellows, and students for a full
day of talks, poster presentations, and networking opportunities. It was the first conference outing for our undergraduate researchers Richie and Sebastien, who were very excited to
be introduced to the concept of conference SWAG. On the day, Nicole brought home an award for best post-doc talk for her presentation entitled “A genomic timescale for placental mammal evolution.”

Texas Genetics Society

Save The Date Poster for the 49th Annual Meeting of the Texas Genetics Society in College Station, TX (2022)In late March the lab attended the 49th Annual meeting of the Texas Genetics Society at The Stella Hotel here in College Station, with Nicole winning a prize for her presentation entitled “Karyotypic stasis and swarming influenced the evolution of viral tolerance in a large bat radiation.”

Biology of Genomes at Cold Spring Harbor

Earlier this year, Andrew and Nicole were shipped North to attend the Biology of Genomes Meeting in the beautiful surroundings of Cold Spring Harbor Laboratories in New York. Aside from all the wonderful science presented at the meeting, the famous CSHL Lobster dinner was a particular highlight. And while a caricature drawing of Andrew and Nicole was not the souvenir Bill was hoping for, it was the one he got!
Lobster dinner with broccoli and potato A caricature of Nicole and Andrew from their trip to Cold Spring Harbour Labs in New York

Team Recombination—Spring 2022 Undergraduate Researchers

Aggie Research Program Undergraduate Researchers in the Murphy Lab in the Spring of 2022Last Spring, we were joined by Sebastian, Zoya, Melinda, and Richie, who spent a semester
in the lab learning basic bioinformatic skills and building recombination maps for various mammalian species, including a gorilla, a fruit bat, a blue whale, and a naked mole rat.

American Genetics Association in Snowbird, Utah

Nicole, Bill and Andrew with Anjanette Baker in the snowy mountains of UtahThe Murphy Lab recently attended the annual meeting of the American Genetics Association in Snowbird, Utah. The theme of this year’s meeting was Conservation Genomics: Current Applications and Future Directions. And as if we weren’t already spoiled by two days of brilliant and insightful conservation talks, we were also treated to a fresh fall of snow! Here
we are with AGA manager-extraordinaire Anjanette Baker on a quick foray out into the snowy mountains.

Isabella Childers joins the lab

Isabella Childers works at a large computer screen“I graduated in 2021 from Clemson University, South Carolina, with a Bachelor’s in Genetics.
In the spring of 2022, I joined the Murphy Lab as a genetics PhD student. I’m currently
working on reconstructing the genome assembly of the aardvark and Hoffmann’s two-toed sloth, which will be used to help reconstruct the ancestral placental mammal karyotype and gene order.”

Congratulations, Drs. Bredemeyer & Myers!

Dr. Alex Myers, left, works at lab bench and right, Dr. Kevin Bredemeyer has a sombrero on at a Mexican restaurant.Congratulations to the newest Murphy Lab Doctors—Dr. Kevin Bredemeyer and (double)
Dr. Alexandra Myers (PhD/DVM) on their recent graduations! Although we’re very sad to
see them go, Kevin is now a Bioinformatic Analyst for Catalytic, and Alex now works as a
veterinary diagnostic clinician in sunny Brisbane, Australia.

Dr. Nicole Foley joins the lab

Dr. Nicole Foley in her officeWe recently welcomed a new postdoctoral associate, Dr. Nicole Foley, to the lab. Nicole obtained her Ph.D. at Emma Teeling’s Bat Lab at University College Dublin, where she worked on the role of
telomeres in bat aging. Nicole is currently studying the role of recombination, hybridization, and chromosome evolution in mammalian phylogenomics as part of a new three-year NSF award to
improve phylogenetic inference.

Dr. Gang Li starts his own lab

Dr. Gang LiCongratulations to Dr. Gang Li, former Murphy Lab Research Associate, who
is starting his new lab at the College of Life Science, Shaanxi Normal
University, in China.

Dr. Victor Mason's Paper in Journal of Heredity

Dr. Victor Mason with the Journal of Heredity coverFormer graduate student Dr. Victor Mason’s paper on Comparative Southeast Asian Biogeography was just published in the Journal of Heredity. His paper describes the
application of genomic tools to museum specimens to infer the evolutionary history and phylogeography of several forest-dependent mammals: Sunda colugos, lesser and greater mouse deer, and Sunda pangolins. This work was performed in collaboration with Dr. Kris Helgen from the University of Adelaide.