Our review paper “Comparative biology needs de novo transcriptome assemblies: drawing attention towards amphibians” has just been accepted and will be out soon in Amphibia-Reptilia! Led by María Torres-Sánchez, and written in collaboration with members of the Amphibian Genomics Consortium, this piece highlights the untapped potential of transcriptomics for amphibian research and calls for broader inclusion of amphibian data in comparative genomics. Stay tuned!

This study, led by PhD student Matteo Di Nicola, is not on the Batrachochytrium fungi but on Ophidiomyces ophidiicola (Oo), a fungus that specifically infects snakes. The research provides a comprehensive overview of Oo’s distribution in Italy, utilizing both contemporary field samples and historical museum specimens. Analyzing 423 snakes across 17 species and regions, the team detected Oo in 32 individuals from five species, notably prevalent in the semi-aquatic dice snake (Natrix tessellata). The study also identified two distinct clades of Oo: Clade I, primarily found in older museum specimens, suggesting a historical presence, and Clade II, prevalent in recent samples, indicating a current advantage. These findings highlight the complex epidemiology of snake fungal disease in Europe and underscore the need for standardized surveillance to better understand and manage this emerging threat to snake populations

This paper marks the first of many in a larger effort to understand the evolutionary history of Eleutherodactylus frogs across the Caribbean—part of an exciting collaboration with Rayna Bell (California Academy of Sciences), USGS, and other partners. In this study, we used genome-wide ddRADseq and mitochondrial data to examine two species from the island of Guadeloupe (E. barlagnei and E. pinchoni), uncovering clear population structure and signs of divergence linked to elevation and historic volcanic activity. The paper was led by Ed Myers and two MSc students at the California Academy of Sciences. These findings lay the groundwork for a larger genomic framework spanning island systems and species groups, with the ultimate goal of better understanding how evolution, isolation, and landscape interact in shaping Caribbean amphibian diversity. Published in Zoological Journal of the Linnean Society:

Excited to share that, together with a fantastic team of collaborators, we’ve been awarded a RIBBiTR grant for 15000$! This project is together with Jack Boyette and Guilherme Becker at Penn State University and Roland Knapp at the University of California-Santa Barbara. Our project will use sequence capture to study the evolutionary history of Batrachochytrium dendrobatidis (Bd)—the fungal pathogen devastating amphibian populations around the world. We’ll be focusing on samples from Brazil and the Sierra Nevada to investigate how Bd strains differ, spread, and impact host communities over time.

Amphibians are among the most evolutionarily fascinating and ecologically threatened vertebrates, yet they remain severely underrepresented in genomic datasets. This paper introduces the Amphibian Genomics Consortium (AGC), a global network of over 280 researchers from 41 countries working to expand and coordinate the generation of genomic resources for frogs, salamanders, and caecilians. The study outlines current gaps, highlights technical and funding challenges, and presents a roadmap for collaborative progress, emphasizing capacity building, data sharing, and inclusivity. By bridging the divide between genomics and conservation, the AGC aims to empower amphibian science worldwide and ensure these species are no longer left behind in the genomics revolution. The paper is published in BMC Genomics

In a temporary(!) detour from amphibians, I did a sidequest into hedgehog genomics and discovered something unexpected. By sequencing the cell-free DNA in the blood of hedgehogs suffering from a mysterious disease (HDD), we identified a previously unknown circovirus. This is the first time a circovirus has been found in the mammalian order Eulipotyphla. With over 60% of sampled hedgehogs testing positive for the virus, its role in hedgehog health deserves serious attention—though we didn’t find a direct link with HDD just yet. Stay tuned.

This story started when a sick Japanese giant salamander (Andrias japonicus) arrived at the Smithsonian National Zoo in DC from Japan but it was impossible to culture the pathogen that was infecting it. Using a novel sequence capture array I designed, we managed to genotype the new strain of Batrachochytrium dendrobatidis (Bd) that was infecting the salamander. Despite multiple failed attempts to culture the pathogen, we successfully recovered and sequenced thousands of fungal genes directly from host tissue. Phylogenetic analysis revealed that the Bd strain belonged to the Asia-3 clade, expanding its known range and highlighting the utility of culture-independent methods for uncovering cryptic fungal diversity. We also applied the sequence capture array to samples from Arizona and successfully genotyped the strains directly from the swabs and toeclips. Read more in the journal of Fungal Genetics and Biology or on the Social Media of the Smithsonian

Led by Amadeus Plewnia and Stefan Lötters (Trier University), this study provides a comprehensive update on the conservation status of harlequin toads (Atelopus spp.), one of the world’s most threatened amphibian groups. Analyzing data from 131 species across nearly two decades, we found that declines continue for the vast majority of species—and that despite more than 30 rediscoveries, not a single species has shown a clear recovery. Persistent threats like habitat loss, chytrid fungus, and climate change are still driving populations downward, and most rediscovered populations remain critically small. The study highlights that current conservation strategies have been insufficient and that more targeted, intensive efforts are urgently needed to avoid further extinctions. Read the full article in Nature Communications Earth & Environment.

Led by Gustavo Pisso-Florez, this study is the result of a three-week field expedition to the Andean mountains of southern Colombia, where we confirmed a previously undocumented population of the rocket frog Hyloxalus pinguis. Long considered taxonomically uncertain and lacking genetic data, H. pinguis was found at two new localities in the Nariño department. We characterized the frog’s advertisement call and provided the first molecular data to place it confidently within the Hyloxalus phylogeny. Our analyses show that H. pinguis is more closely related to H. delatorreae than to H. pulchellus, clarifying its evolutionary position and supporting its species status.

Time for a new challenge! I obtained an FWO Junior Postdoctoral Fellowship from the Flemish Government and will spend the next three years at Ghent University working on the genomics of Bsal immunity. This will be done with Professors An Martel and Frank Pasmans who originally discovered Bsal and lead the Wildlife Health Ghent Group. Excited for this new chapter and a move to a new country, but this time not a new language :).

In this study, we peered into the shadows of General Davis Cave to explore the mysterious lives of two salamander species. Using genomic data, we showed that Gyrinophilus subterraneus—a rare, cave-restricted salamander—is still its own thing, despite occasional underground flirtations with its surface cousin, G. porphyriticus. These two lineages coexist and even produce the odd hybrid (just first-generation hybrids), but remain genetically distinct. It’s a compelling case of sympatric speciation in a hidden corner of Appalachia. Conservation-wise, though, things are a bit murky: G. subterraneus may be in decline, highlighting the importance of keeping a close eye on this rare species.

Turns out, some salamanders have different parenting styles. In this study, we show that giving birth to live young — rather than delivering larvae — has evolved independently multiple times in the fire salamander genus (Salamandra). Using phylogenomic data, we found that these shifts to so-called pueriparity happened across different branches of the family tree and at different timescales. It’s a striking example of how the same extreme life history trait can pop up more than once — and a reminder that even within a single genus, evolution can be a little unpredictable. The full story is in Molecular Phylogenetics and Evolution:

Our recent study investigates the evolutionary history of the São Tomé caecilian (Schistometopum thomense), a rare, legless amphibian endemic to São Tomé Island in the Gulf of Guinea. Despite their secretive, underground lifestyle, these animals show clear signs of historical divergence across the island, likely shaped by volcanic activity and habitat fragmentation. Using genome-wide data, we found evidence for deep genetic splits between populations, followed by secondary contact and gene flow — a dynamic history of isolation and reconnection. The findings highlight how island landscapes and life-history traits interact to drive evolutionary patterns, even in species that are rarely seen. The paper is published in Molecular Ecology/

Unlock the genetic secrets of the past! Our recent research demonstrates a powerful new technique to extract valuable genomic information from decades-old museum specimens, even the seemingly unusable remnants of past analyses. Thanks to the foresight of Addison Wynn, who wisely preserved the "waste" from allozyme extractions dating back to the 1980s, we can now access a wealth of genetic data previously thought lost. This breakthrough opens exciting new avenues for understanding population history, evolution, and conservation using irreplaceable historical collections.

The defence was online due to COVID restrictions, but after a presentation and two hours of questioning its now officially Dr. Kevin! Big thanks to the opponents Miguel Vences, Kathryn Elmer, Rui Rebelo and José Melo-Ferreira and for everybody who listened to me talk about amphibian genomics on youtube for a few hours. Now a one month break and then time to start a postdoc at CIBIO and continue working on these amazing critters.

It has been a long few months of covid lockdowns and thesis writing lockdowns, but I finally handed in my thesis! Its been quite a few years but very happy with the final product. Obviously a big thank you to my Advisors and all other co-authors, friends, family and every person and amphibian that helped out in this process. You can find a lot more words on that in the acknowledgements, and a lot more words on amphibian genomics in the other few 100 pages.

The rocky islets of the Bahamas—famous from Jonathan Losos’ pioneering work as a natural laboratory for studying evolution in action—continue to reveal new insights. In this study, led by Johanna Wegener at the University of Rhode Island, we explored 16 island populations of brown anoles (Anolis sagrei) and found that higher population densities were linked to more frequent injuries and relatively longer heads—traits associated with biting and social dominance. Notably, these patterns were found in both males and females, challenging the assumption that competition-driven morphological evolution is a male-only affair.

This paper led by Christophe Dufresnes and Glib Mazepa at the University of Laussane investigates the evolutionary history of Bufotes toads across its range using ddRAD sequencing and mitochodrial hapotypes exploring many of the fascinating aspects of this study system such as allopolyploidization and high mito-nuclear discordance. It also describes two new species B. cypriensis and B. perrini.

One of my first projects as a geneticist was on one of the most range-restricted vertebrates in the United States, the Shenandoah salamander. This cute critter might looks similar to its sister species, the omni-present redbacked salamader but is adapted to only three mountaintops in Virginia. We compare genetic diversity to landscape features to try and figure out what restricts its dispersal. Another fruitful collaboration with Evan Grant's lab at USGS!

Our paper on the relationship between MHC genotypes and Ranavirus infection in Maryland woodfrogs is out in Immunogenetics! Started as a small side-project many moons ago now finally published thanks to hard work by the co-authors Anna, Carly, Rob and Evan!

The tortoise paper strikes again. We won the Smithsonian's Secretary Research Award and were presented with a plaque at a breakfast "gala" at the American History Museum by Secretary Skorton.

Our paper on the effects of translocations on male Desert tortoise fecundity won the Robert C. Stebbins award at the annual Desert Tortoise Council Conference! Rob Fleischer gave the plenary talk to an audience including tortoise researchers, wildlife managers and tortoise enthusiasts.

Thierry Chambert's manuscript on occupancy modelling has been published in the journal Methods in Ecology and Evolution! The paper describes a new model that includes species mis-identification error and nondetection to improve occupancy models. We provided the genetic data for the Species ID for two closely related Plethodon salamanders that are sometimes misidentified in the field due to their similarity and overlapping habitats.

Our paper on MHC variation in Rana chiricahuensis was published in the journal Conservation Genetics. We genotyped adults across the US range to describe the MHC variation in the species and also genotyped over 250 metamorphs just before their release from the captive breeding facilities at the Phoenix Zoo. When we went back to catch the survivors a year later we found an association between over winter survival (when Bd infections are high), and the type of MHC-allele the froglets had.

For this paper published in the journal Developmental and Comparative Immunology we developed primers to sequence the entire exon 2 and parts of the flanking intron for the MHC class II locus across several genera of Ranid frogs. We tested them using both Sanger, 454 and Illumina sequencing and describe the diversity we found across 18 different species with notes on selection and trans-species polymorphism.