Updates
4 Feb 2021: This past year has really challenged all of us. We have seen research come to a halt with lockdowns and modifications to maintain our own health. We have been able to keep a small part of the work moving foward and saw research resume, albeit at reduced levels. Now, limitations of resources are the challenge as supplies and reagents are backordered for months on end, as we try to find new vendors with the same items we need to continue our work. In the interim, we have received support from the USFWS, through a recommendation from the National Academy of Sciences, to focus on red wolves. Lead by Dr. Kristin Brzeski, we are now supported to conduct a genetic survey in the American southeast. We are working in collaboration with Drs. Ben Sacks and Laurent Frantz, who will be exploring ancient DNA sequencing as well. Both perspectives are expected to give us huge advances in understanding red wolves and coyotes in North America. We are excited to receive such support and are moving forward with developing methods, resources, and collections. Our focus is to continue with admixture/ancestry genetics, genome sequencing, and evolutionary models of demography. We are also extremely excited about welcoming Amy Shutt to our Team! She's an incredible member and has really helped us expand our community connections. We also were able to hire Joey Hinton for field work. Finally, we also welcome Drs. Bill Murphy and Anna Linderholm (Texas A&M) to the team of collabortors -- both of whom have significantly contributed to our research program. All of these steps forward are tremendous. I look fowrad to giving updates soon about our efforts.
-B vonHoldt
4 August 2020: Congratulations to Dr. Allie DeCandia! She has completed her Ph.D. program and is now off to join the Smithsonian as a post-doctoral researcher with Dr. Klaus Koepfli. I look fowrad to keeping our collabortions going but also to the new contributions you will make to the field. Keep it up!!
-B vonHoldt
5 June 2020: Although Liz Heppenheimer has since graduated and moved on in her career, she recently published the last project of her Ph.D.! Her work can be found here: Citation: Heppenheimer et al. (2020) A genomie-wide perspective on the persistence on red wolf ancestry in southeastern canids. Journal of Heredity 111(3), 277-286 [abstract]. We also are underway in working to complete the assembly of a coyote reference genome! This will provide a significant insight into the patterns of shared genetics and evolutionary history of North American canids.
-B vonHoldt
2 Jan 2019: Due to a flurry of manuscripts, revisions, and proofs, our fall was quite busy! We have now published three papers as a result of population genomic analysis of North American canids. This is only the beginning of the genetic investigations into the current composition of our local canines. We are continuing on in our sample collection, sequencing, analysis, and manuscript prepartion. We continue expanding our collaborative community and are always thankful for their involvement! Without them, this effort would not be possible. Happy New Year!
-B vonHoldt
20 Sept 2018: We have been working hard on a number of manuscripts. The first one has just been posted on the public pre-print site BioRxiv and can be found here. It is not published or peer-reviewed yet but we are working on that process right now. We should soon also be submitting a manuscript on coyote demographic genetics and another one on the landscape genetics of wolves of the Great Lakes and southeastern Ontario regions.
-B vonHoldt
2 May 2018: I've been in lab, working alongside Liz and Kristin, preparing loads of canids for sequencing! It's been a great effort. Also, in the past month, we've had to say farewell to Kristin Brzeski as she is embarking on her new Assistant Professorhip at Michigan Tech [website]! Congratulations! Although she will no longer be in the next room over from my office for easy visiting, she continues to play a major role in the Canine Ancestry team. We are excited for her next adventures, and hope to get her back for visits every now and then!
-B vonHoldt
4 Jan 2018: A new publication about coyotes! My graduate student Liz Heppenheimer (also lead for the NA Canine Ancestry project) just published on coyote demography using microsatellite data in the journal Heredity. Check out the paper's abstract here! Great work, Liz!
-B vonHoldt
20 Sept 2017: 
Apologies for the silence. The project has experienced a large change. We are sad to see the departure of Linda Rutledge as the leading researcher on this effort. Though clealry still involved, we have two new leaders for the project, Liz Heppenheimer and Dr. Brezski! Workign with Linda, we have spent time shifting data and analyses to the new team leaders and are soon to be finished with processing the inital rounds of anlayses. Liz will be at The Wildlife Society meeting next week in New Mexico (Picture: on left, Kristin; right, Liz) talking about really intriguing work on coyote population genetics. Make sure to check out that session (Sept 25th symposium session on Genetics to Genomics: What We’ve Learned over the Last 10 Years and What’s Next for Wildlife) organized by our very own Dr. Brzeski! I look forward to being able to post an update in the very near future. For now, we continue to expand our collections, with all of our gratidute to those donating samples. This effort would not be possible without the community's support.
-B vonHoldt
17 May 2017: Just received our project mugs! 
Thanks to Julie Johnson's original design for us. We now have awesome places to put coffee or tea! We also are adding to the breadth of our coyote samples in the North American Canine Ancestry project. After Liz's recent effort, we are appraoching 1000 coyotes. This will provide us with an incredible opportunity to explore local and continent-wide population signatures. The excitement is growing and hopefully soon we will be able to share some good news of results.
-B vonHoldt
17 May 2017: Our paper is out in Journal of Heredity and we got the cover image! Abstract: Reduced fitness of admixed individuals is typically attributed to genetic incompatibilities. Although mismatched genomes can lead to fitness changes, in some cases the reduction in hybrid fitness is subtle. The potential role of transcriptional regulation in admixed genomes could provide a mechanistic explanation for these discrepancies, but evidence is lacking for nonmodel organisms. 
Here, we explored the intersection of genetics and gene regulation in admixed genomes derived from an experimental cross between a western gray wolf and western coyote. We found a significant positive association between methylation and wolf ancestry, and identified outlier genes that have been previously implicated in inbreeding-related, or otherwise deleterious, phenotypes. We describe a pattern of site-specific, rather than genome-wide, methylation driven by inter-specific hybridization. Epigenetic variation is thus suggested to play a nontrivial role in both maintaining and combating mismatched genotypes through putative transcriptional mechanisms. We conclude that the regulation of gene expression is an underappreciated key component of hybrid genome functioning, but could also act as a potential source of novel and beneficial adaptive variation in hybrid offspring. [Citation: B vonHoldt, E Heppenheimer, V Petrenko, P Croonquist, LY Rutledge (2017) Ancestry-specific methylation patterns in admixed offspring from an experimental coyote and gray wolf cross. J Heredity 108(4), 341-348]
-B vonHoldt
7 May 2017: A brief outing with Liz Heppenheimer to see the local Trenton Dog Show! Though it is hard to have a favorite, I was fond of the Old English Sheepdogs!
-B vonHoldt
27 April 2017: I apologize for the lack of entries! It has been a busy past few months. 
Liz Heppenheimer is working hard to add a few hundred coyotes to the growing number of samples we have sequenced. Linda is working through analysis of that full scope of the project. We have a number of new contributors to add to the group. Many people strongly support coyote and wolf genetics, and we continue to work towards understanding more about their ancestry, population dynamics, and evolutionary past. The Princeton team also recently was involved in running a kid activity table the the Princeton's March for Science on Earth Day, 2017. We help teach kids of all ages about genotypes, phenotypes, and dogs! My post-doc Kristin Brzeski and grad student Liz were excellent. [Photo, in order from left to right: Kristin Brzeski holding Lulu, Bridgett vonHoldt, Liz Heppenheimer]
-B vonHoldt
29 Dec 2016: The first North American International Canine Science Conference is open to scholars from all over the world studying all aspects of all species of canines. Check out their website!
-B vonHoldt
22 Nov 2016: A great new article by Elizabeth Pennisi in Science about our changing views on the "tree of life"! As her article opens...."Species were once thought to keep to themselves. Now, hybrids are turning up everywhere, challenging evolutionary theory." She further discusses several examples of species that have experienced (or continue to) gene flow. She ends with acknowledging how biologists have yet to fully understand how hybridization and introgression drive evolution, and how we need to reconcile these processes with the traditionally references view of species as diversifying and diverging over time. The last sentence she quotes Dr. Rieseberg: "It's the world of hybrids...and that's wonderful."
-B vonHoldt
13 Oct 2016: A feature about research from Fordham and the Gotham Coyote Project in the Village Voice!
-B vonHoldt
5 Oct 2016: A grand time last night appearing on the Princeton's WPRB radio show These Vibes Are Too Cosmic, hosted by Stevie and Brian. Thanks for inviting me -- it was great fun! Any time I get to talk about epigenetics and canines is a good time. PLUS, this website is up for just about a year now! What great success! We are in the midst of data analysis and some smaller projects are in the manuscript writing stages -- but overall, I'm still as excited as ever with this great set of collaborators and research questions.
-B vonHoldt
26 Sept 2016: Thanks to the beautiful illustration by Julie Johnson at Life Science Studios (link), we finally have a logo for our project! 
-B vonHoldt
16 Sept 2016: I've been invited to help organize the Smithsonian's inaugural Global Biodiversity Genomics Conference to be held in Washington, D.C. in Feb 2017 (link). Mark your calenders!
-B vonHoldt
11 August 2016: Spent a great day yesterday at the American Museum of Natural History talking about canid domestication and admixture to George Amato's group. A lovely time meeting people, chatting science. Even was able to see Mark Wecklel again, and meet Chris Nagy! Overall, an excellent day.
-B vonHoldt
8 August 2016: Really great read in the recent National Geographic about coyotes! They are a tremendous species and we still have a lot to learn about them. Hopefully our genetic efforts will contribute to the growing body of studies on these animals.
-B vonHoldt
12 July 2016: Big push to get the last few samples loaded onto the sequencer. It's great to see the lab working hard on sample organization and preparation. We are excited about getting the analysis underway and working to detail histories of admixed populations! Stay tuned!
-B vonHoldt
9 June 2016: It has been a busy last month to say the least! Linda continues to organize, curate, and sequence upwards of >1000 canine samples! We have spent many hours discussing canines with collaborators and ecologists -- working to keep in touch with everyone. The summer months mean many people are in the field, at conferences, or abroad. My group has been very active in attending conferences and making/keeping connections. Keep up the energy, everyone!
-B vonHoldt
1 May 2016: 
After the NENHC last in late April, I was lucky enough to travel to Yellowstone with Liz and Allie, both my graduate students! The trip was work-related to meet with all colleagues conducting research on the Yellowstone gray wolf, but as always, there must be some fun involved. Liz and I are regulars at the Park but this was Allie's first trip. We also traveled with Robert Wayne and Kirk Lohmueller (UCLA), Andy Dobson (Princeton Uni), Pete Hudson (Penn State), Tim Coulson and Sonya Clegg (Oxford), and a number of others. We also were intrigued by a rare viewing of two coyotes...a presence that has decreased with the recovery of gray wolves in the Park. It was also calving season so the landscape was peppered with brand new bison calves! Though it was a chilly week, we saw many amazing sites and enjoyed socializing. [Photo, in order from left to right: Allie DeCandia, Liz Heppenheimer, Bridgett vonHoldt]
-B vonHoldt
24 April 2016: 
The lab traveled to the Northeast Natural History Conference where Kristin, Liz, and myself each gave a short talk on canids! Kristin spoke about the current controversy of the red wolf; Liz discussed some recently results of her genetics work on eastern coyotes; I gave a quick presentation of a recent paper I published with some other NA Canine Ancestry colleagues on admixture mapping in North American canids (soon to have proofs released in Molecular Ecology). As conferences are a great place to meet people, we were also able to meet the Gotham Coyote Project and are happy to add them to the growing list of collaborators. Though it was a very quick weekend at the conference, our goal is to keep reaching out to canid researchers and establish a contient-wide network to move the field forward through positive connections. We also have received a welcoming response from the UW-Madison Urban Coyote Project. Coyote genetics is really an amazing field. [Photo, in order from left to right: Bridgett vonHoldt, Liz Heppenheimer, Allie DeCandia, Kristin Brzeski, Linda Rutledge]
-B vonHoldt
11 April 2016: 
Extracting DNA from coastal British Columbia wolf teeth from Chris Darimont. Also prepping plates of eastern wolf, gray wolf, and coyote DNA for RADseq DNA libraries from Canadian provinces.
-L Rutledge
13 March 2016: We continue to receive samples and new collaborations for this large-scale research effort. We recently had an excellent and very productive conference call with Drs. Ben Sacks and Steve Fain. I'm thrilled to be able to welcome them to the group as their expertise and input is highly valued. We also have welcomed Dr. Klaus Koepfli to the team, as his endless knowledge has always provided insights. Further, Linda is energetically and rapidly screening samples for sequencing, with very promising preliminary results! I am thrilled to be working with so many excellent researchers.
-B vonHoldt
23 Feb 2016: We recently collected more coyote samples in Pennsylvania that were part of a state-supported event. Our presence there allowed us to interact with people and discuss how the contribution of a donated sample will help provide a broader insight into the genetic variation of eastern coyotes. Though we are not making any political statement about these events, many (if not all) states with coyotes have some level of these events to manage this species. These events are held regardless of our presence but allows us to explain our research to the public, and hopefully experience positive communication about genetics with them. We feel lucky that these canids can ultimately contribute to research and expand our knowledge of canine genetics.
-B vonHoldt
11 Feb 2015: 144 more wolves and coyote now being sequenced! Also excited to add Chris Darimont (University of Victoria), Ben Sacks (UC Davis), and Steve Fain (USFWS) to our list of collaborators.
-L Rutledge
1 Feb 2016: 
A field photo shared by collaborator Dr. Joey Hinton (pictured right: Jennifer, Mark, and Rusty collaring a coyote). His team of collaborators are conducting a spatial ecology project on southeastern coyotes. I remain always grateful for their willingness to share and collaborate. They are an exceptional team of researchers! Keep up the excellent work!
-B vonHoldt
28 Jan 2016: Recently feel like our project may have global reach -- our project's webpage was just mentioned on canids-l (the mailing list of the IUCN SSC Canid Specialist Group)! Thank you Neil Hutt (Red Wolf Coalition) for spreading the word! Hopefully this will help us reach all groups interested in canine ancestry beyond North America. I look forward to the continued discussions on canines!
-B vonHoldt
14 Jan 2016: Happy New Year! We are off to a great start after receiving another batch of canine samples from a collaborator...keeping Linda busy! We also are beginning to plan our upcoming sample collection season for Pennsylvania coyotes, and hopefully a trip south to Mid-Atlantic to attend a few fur trading events. All looks great on the horizon for canine research!
-B vonHoldt
7 Dec 2015: Another really nice article in New Republic discussing the focus on red wolves and efforts towards understanding its origin and species status. Additionally, if hybrids aer present, we often lack the regualtory framework for knowing how to manage them. I hope our efforts will soon provide a wider, deeper insight into North American's canine ancestry.
-B vonHoldt
1 Dec 2015: Another article in Technician Online discussing the presence, nomenclature, and perception of the eastern canines. Their origins, insights into ancestry, and how natural selection is acting on admixture are some of the key questions we will be able to address with our sequenicng efforts. Canines are in the news...!
-B vonHoldt
20 Nov 2015: 
I'm not afraid of getting my hands dirty (pictured right)! Handling some coyote livers graciously donated by a collaborator! Very stinky samples but these coyotes will be critical for capturing the genetic variation representing the southeast.
-B vonHoldt
13 Nov 2015: The "coywolf" issue is really exploding on the internet and social media. My colleague Roland Kays has just written a nice piece in The Conversation that highlights some details and critical aspects when thinking about admixture and hybridization. There is a distinct difference when considering an evolutionary lineage that carries signals of past admixture and that of recent hybrids (e.g. F1s). Though both events result in a detectable signature, they have different implications for how we perceive (and perhaps, ultimately regulate) these populations. It's always more complicated than just a simple label...!
-B vonHoldt
9 Nov 2015: Working to establish more connections with western US states to hopefully include representatives across North America. Currently in correspondance with Texas, Colorado, Wyoming, and the southwest. Any scale of contribution helps, even a handful of samples. Linda is analzying our pilot data to ensure that the sequencing method is spot-on and about to submit a new set of samples to ensure library preps are also perfected. Stay tuned for more updates!
-B vonHoldt
2 Nov 2015: 
Yesterday, members of the vonHoldt lab set up a scientific table at the New Jersey Fur Harvesters Annual Convention! This was a great opportunity to talk to trappers and explain the type of research we are doing. This interaction also served as a way to establish a connection with the trapping community and show them how easy it is to contribute to science through a small sample donation from samples acquired through their regular harvest practices.
-B vonHoldt
27 Oct 2015: Just powering through DNA quality control - getting ready for library prep of hundreds of samples. And more to come!
-L Rutledge
24 Oct 2015: We have been invited to have a scientific table at the New Jersey Fur Harvesters Annual Convention next weekend! This is a great opportunity to talk to trappers and explain the type of research we are doing. I envision this interaction as a way to establish a connection with the trapping community and show them how easy it is to contribute to science through a small sample donation.
Plus, we're updating our sample map! Check it out.
-B vonHoldt
21 Oct 2015: Welcome to our new website! This site is dedicated to a large, multi-institutional research effort to explore and understand the ancestry make-up of canines across North America. With the combined forces of many experts, we expect this to be an incredibly successful effort that produces incredible insights into the lives of canines. Please be patient as we develop our website! We will have regular update posts to keep you abreast of our progress, new collaborations, public talks, and results as research continues. Remember, it is a never-ending effort and we will do our best to report back our findings! Thank you for your support in the meantime.
-B vonHoldt