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Zachary G. MacDonald

@drzacmacdonald

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🧬Conservation Genomics and Biodiversity
🎓Assistant Professor, University of California Riverside
🦋 🐝🪲🐞Entomologist
Real science from actual scientists

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🦋 Scientists Discover New Butterfly Species with Streamlined Genome After 40,000 Years of Isolation 🧬
🦋 This butterfly survived the last Glacial Maximum ❄️ in a tiny refuge in southwestern Alberta 🇨🇦 and now persists in Waterton Lakes National Park 🏔️, isolated from other populations by more than 400 km. Its extreme isolation has produced a unique evolutionary history, with the species streamlining its genetic code 🧬 through extensive purging of deleterious genetic material from its genome.
🌍✨ This work highlights the importance of using whole genome sequencing 🧬 to establish guidelines for effective conservation actions.
Lead author Zachary MacDonald explains: “Using genomics, we also discovered that this population has been small, isolated, and likely genetically depauperate for up to 40 thousand years. It is also very ecologically divergent from other populations, leading us to describe it as a new species. It's an amazing example of how populations, and even entire species, can survive with little genetic variation, so long as their "load" of deleterious genetic variation is low.”
MacDonald went on to highlight the importance reference genomes: “A greater abundance and diversity of reference genomes directly translates to more economical and impactful conservation science; particularly, in lesser known and understudied taxa. We need more reference genomes, and we need them fast.”
📸 All photos courtesy of lead author Zachary MacDonald 🦋 @drzacmacdonald

🦋 #NewButterflySpecies | 🧬 #Genomics | 🌍 #Conservation | 🏔️ #WatertonLakes | ⚖️ #GeneticDiversity | 📜 #Evolution | 🔬 #WildlifeResearch | 🌱 #Biodiversity | ⏳ #SurvivalStory by @drzacmacdonald

Some behind-the-scenes photos and notes from our recent field trip to California’s Sierra Nevada, searching for the highest butterflies in North America with filmmaker Aaron Lemle and student Kentaro Matsunaga.

Three alpine species occur here and nowhere else on Earth: the Sierra Nevada Parnassian, the Sierra Green Sulphur, and the Ivallda Arctic. Two years ago, to my great surprise, I discovered a population of Ivallda Arctic on the summit of Mt. Whitney (14,505 ft, shown in last two photos), marking the single highest butterfly population in North America north of Mexico. Despite heavy traffic at the summit, this population had gone unnoticed until then. We infer it to be relatively new, reflecting the upslope movement of butterflies tracking changing climatic conditions. That strategy works only temporarily and now they are clearly out of space.

This summer we extended our work with an expedition to the summit of Mt. Langley, searching for additional populations of the Ivallda Arctic. These butterflies live in such extreme environments that it takes two full years to complete their life cycle, meaning they only fly every other year. We must make the most of those rare flight seasons to conduct our surveys. To our surprise, we found the Sierra Nevada Parnassian on the way up (very far south for this species) and then the Ivallda Arctic right at the summit, marking the second highest butterfly population ever recorded in North America and the very southernmost.

Kentaro just completed a wonderful undergraduate thesis predicting how these three endemic alpine butterflies may shift their ranges over the next century. The results are both fascinating and a bit grim, and we look forward to sharing them in his first publication. We are also excited to continue working with Aaron on his documentary, which will showcase these butterflies along with our science and conservation efforts.

This short expedition marked the end of my long 12,000-mile field trip, from Los Angeles to the northern Yukon. The @toyotausa #4runner was bulletproof. Unbelievable, all the diversity to be observed, studied, and conserved, particularly in small packages, like butterflies. by @drzacmacdonald

This is the Quino Checkerspot butterfly (Euphydryas editha quino), a federally endangered subspecies. Before the 1980s, this was probably the most abundant butt in Southern California. However, due to habitat loss, competitive exclusion of host plants, warming/drying climatic conditions, and a general lack of love, the Quino is now one of California’s most imperiled butts. This little guy will be among the first specimens to be sequenced as part of our California Conservation Genomics Project. We’ve been working on a chromosome-level genome assembly for E. editha, which is basically a map showing the identity and location of every DNA base pair in the species’ genome (there are probably between 500 million and 1 billion base pairs in this species). This is similar to the Human Genome Project, but for a butt instead. Next, we’ll sequence the entire genome of tens to hundreds of individuals to infer some things/stuff; e.g., are populations divergently adapted to feed on different host plants and/or thrive in slightly different environments? and is the evolution and spread of novel genetic adaptations likely to help populations persist as our climate continues to change (“evolutionary rescue”)? These inferences will guide conservation practice and inform ongoing translocation and captive breeding programs. Not only is the conservation of this butt intrinsically important, but it is also instrumental, providing a mechanism for protecting what little natural landscapes remain in Southern California. by @drzacmacdonald

Signed in by Nixon in ’73, the US Endangered Species Act (ESA) is, or was, the most rad piece of conservation legislation in the US, possibly the world. It protected endangered species not only from direct harm (e.g., being shot or run over), but also from destruction of their critical habitat. This week, the US Fish and Wildlife Service and NOAA Fisheries changed their definition of harm such that habitat destruction will no longer always count. The ESA still exists, but one of the protections that made it so powerful has been significantly weakened. Habitat protection can restrict development and resource extraction, but it’s also saved countless species and wild landscapes. Things like climate change are major threats, but habitat loss remains, by a massive margin, the biggest direct driver of biodiversity loss.

We live in a time with powerful new tools for quantifying exactly what habitat matters most, and what can be sacrificed to development. Pictured is a habitat suitability analysis for the endangered Quino Checkerspot (Euphydryas editha quino) in Southern California. This is a useful first sweep, using ecological, environmental, and geographical associations of known occurrences to predict which areas comprise suitable habitat. Quino was once common across much of SoCal, but habitat loss and fragmentation eliminated most of its range before it was listed in 1997. Invasive plants and climate change have added to the problem, but habitat destruction is at the core of the butterfly’s decline. We’re now layering on whole-genome sequencing to identify where habitat matters most, which populations are threatened by low genomic diversity, and where the butterfly’s genomic strongholds remain. We’re putting the final touches on the first diploid chromosome-level genome assembly for Euphydryas editha and hope to have whole genome analyses underway within the next few months.

To be clear, as a Canadian working in the US, I’m not interested in political orientation or criticism of any administration on platforms like this. I’m interested in the best path forward within our limitations, using the best science to conserve endangered species. by @drzacmacdonald

New paper out on genomics, ecology, and conservation of the American rubyspot damselfly, Hetaerina americana.

As part of our California Conservation Genomics Project, we use our recently assembled H. americana reference genome and generated whole-genome resequencing data for more than 130 individuals. Hetaerina americana has a broad distribution, found in small streams across much of the continental US, and has long been assumed to be a single but variable species. Although some declines have been observed across the western portion of its range, the species was still considered of least conservation concern on account of its broad distribution.

Using whole-genome analyses integrated with comparative niche and morphological modelling, we show that there are at least three deeply divergent lineages in California. Landscape genomic modelling shows us that habitat connectivity drives genomic structure within each. This is a notable result for insects--in many past analyses we have found that only geographic distance or differences in environmental conditions determine gene flow among populations. That is not the case here, where the connectivity and quality of little streams really matter. This inference is important because, across much of California, streams are some of our most threatened habitats, and these damselflies may be in trouble. Average genomic diversity in the California lineages appears to be about one-half to one-third of what it is across the nominally widespread species, raising significant conservation concerns.

Open access (free to read): MacDonald, Z. G., Beninde, J., Dupuis, J. R., Gillespie, T. W., Shaffer, H. B., & Grether, G. F. (2026). From lineage discovery to conservation prioritisation: An integrative genomic framework applied to a model damselfly system. Molecular Ecology, 35, e70385. https://doi.org/10.1111/mec.70385 by @drzacmacdonald

Our 200-gallon peninsula is starting to emerge from the dreaded ugly phase... still plenty of brown algae and Acropora not exactly thriving. But this trio of captive-bred yellow tangs from @biotaaquariums has at least made our tank something worth looking at again. As our lights dimmed for the evening, I spent a good hour with the OM-1 trying to photograph Earl, Perl, and Swirl (@dani_mariea in charge of names). Also pictured is our rad new elegance coral, also from Biota.

I’ve been keeping aquariums at home for about 30 years, and at work, I research and teach conservation biology. From a conservation perspective, there's an obvious paradox to reef keeping--while the whole point is appreciating biodiversity, a long history of collecting wild fish and corals has caused real damage. IMO, aquaculture of both fish and corals is the best path forward, and it’s sweet to see groups like Biota making it work at scale.

Yup, captive-bred fish sometimes cost a bit more upfront, but once losses from wild-caught fish (and guilt associated with it) are accounted for, I figure it's a wash. CB fish come in cleaner, adapt quicker, eat easier, and disease risk is I think quite a bit lower. If I tried to quarantine (QT) all five of our Zebrasoma tangs properly, there’s no way we could introduce them together (required for territorial reasons). All our biota fish went straight into the display, no QT and no issues so far. Not suggesting anyone skip QT, but I just set up my first QT, and it sucks.

To be clear, some of our fish are wild caught (from sources that I hear are reputable and possibly sustainable). But I think we're really moving in the right direction with these captive breeding programs.

@innovative.marine @reefbreeders @biotaaquariums @omsystem.cameras by @drzacmacdonald

Female crab spider, likely Mecaphesa. Instead of building a web, this spider waits on flowers for nectar-feeding insects to land, then grabs them with its enlarged front legs and subdues them with venom. Not harmful to people, but deadly for insects unlucky enough to stop by. Some flower-dwelling crab spiders shift between white and yellow to better match the flower they’re sitting on--this one was in Encilia, and thus yellow. by @drzacmacdonald

Evening walk on our local trail and @dani_mariea and I found this fuzzy little bear scarab beetle, Paracotalpa ursina, munching and then trying to escape my lens under an Encelia flower. Splendor awaits in minute proportions, as some random guy once said.

15 focus-stacked shots on an OM-1 by @drzacmacdonald

Happy SuperbOwl Sunday.
Northern pygmy owl (Glaucidium gnoma), photographed with @john.acorn.7, years ago, in north-central Alberta ("pygymy corner", a desolate place, which I'm continually surprised exists even when I'm not there).
About the size of a pop can. Completely lethal. These fluffs regularly kill prey close to their own body mass (mass, not size, since they are indeed mostly fluff). Diet is dominated by small mammals, like voles and mice. In winter, survival depends on frequent hunting to maintain metabolism and body temperature, even in −40 °C. by @drzacmacdonald

First time teaching General Entomology. About 80 students, most seeming entirely stoked about the incredible biodiversity and opportunity for discovery before them 🦋 by @drzacmacdonald

Much family debate on natural history vs fine art museums lately. One perspective is that natural history museums are deeper, more meaningful, and more capable of inspiring learning and awe because they interpret a reality that extends beyond human constructs into deep time and evolutionary processes, where closer inspection of pattern and form consistently reveals greater complexity and facts that extend far beyond, and help us understand, human experience. As layers of any natural history object are examined, additional complexity becomes apparent, and increased scrutiny reveals ever more intricate detail. Through this examination, it becomes possible to infer both macro and micro evolutionary processes that generate and maintain life, while also tracing the human, historical, and social contexts through which such processes were discovered, allowing insight into both the external natural world and our internal one. By contrast, much contemporary fine art is fundamentally self-referential, concerned primarily with the artist, the market, and human interiority (and possibly superiority), rather than anything larger than the human experience. Human made objects can be interpreted only through their emergent properties (which natural objects also possess) and closer inspection almost always exposes imperfections that are instructive only of human limitation rather than ability. Attempts to infer generative processes from the form of human made objects often disappoint, as underlying means of construction are prosaic and constrained, and often implicate some form of moral compromise, whether artistic vanity, corporate profit, or exploitation embedded in the materials and labor used. Counter points in comments, and all thoughts welcome. by @drzacmacdonald

Podcastin about insect conservation with Dr. Hollis Woodard @crotalus.ruber 🤘🦋Can I Bug You Podcast: @ucrbugpod by @drzacmacdonald