Nicolas Alexandre
@nicmalexandre.bsky.social
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Reposted by Nicolas Alexandre
msbbirds.bsky.social
New paper on ecosystem-wide PFAS contamination at Holloman AFB, New Mexico

authors.elsevier.com/c/1lAOb3Ao6B...
Winter evening at Holloman Lake, New Mexico
nicmalexandre.bsky.social
That’s a good question! Let me look into my publishing agreement and see if there’s something I can do! But in the meantime, send me an email!
nicmalexandre.bsky.social
Send me an email [email protected]

Big fan by the way!❤️
Reposted by Nicolas Alexandre
lizzysteell.bsky.social
Excited to share an invited commentary about the fantastic and ambitious work by @nicmalexandre.bsky.social and colleagues in @globalchangebio.bsky.social on Anna's Hummingbird beaks. It was a joy to write about, congratulations on a super cool study!

onlinelibrary.wiley.com/doi/10.1111/...
Fitting the Bill in an Urban World: Hummingbird Beak Shape Responds to Anthropogenic Factors
Click on the article title to read more.
onlinelibrary.wiley.com
nicmalexandre.bsky.social
Take a look at @science.org's article describing our work in
@globalchangebio.bsky.social showing that beak morphology of hummingbirds has changed in association with feeders!
science.org/content/arti...
nicmalexandre.bsky.social
Finally I wanted to thank the Museum of Vertebrate Zoology (Shoutout to curator Carla Cicero), the U.S. Census, Christmas Bird Count, PRISM Climate Group, and Newspapers.com for the resources that have been made available.
Historical Newspapers from the 1700's-2000s
The largest online newspaper archive. Used by millions every month for historical research, family history, crime investigations, journalism, and more.
Newspapers.com
nicmalexandre.bsky.social
I also want to thank our fearless mentor, Prof. Alejo Rico-Guevara who has kept the passion alive throughout. And thank you to the best co-leads authors ever, PhD students Simon English and Faye Romero who made this process fun!
nicmalexandre.bsky.social
We are so grateful to Prof. Laura Stein for her advice on modeling, and to CJ Battey @cjbattey.bsky.social for his help with data acquisition and analysis. We are indebted to Grieg et al. & Battey et al. for their foundational work that inspired this project.
nicmalexandre.bsky.social
Huge thanks to undergrads who made this work possible: Timothy Barnes, Audrey E. Smith, Saron Akalu, Haarini Sridhar, Gillian Montross & Ezra Collins.👏👏
nicmalexandre.bsky.social
To test this, Prof. Don Powers @lampornis.bsky.social showed hummingbirds actively heat their beaks after flight. Turns out, the bill helps dissipate heat during perching! 🔥➡️💨
nicmalexandre.bsky.social
But climate matters too. Using PRISM data, we found that in cooler areas in the north, beaks are shorter, smaller, and deeper, consistent with thermoregulation theory. ❄️☀️
nicmalexandre.bsky.social
Collaborating with Prof. Zoe Migicovsky @zoemig.bsky.social , Alejandro Rico-Guevara, Felipe Garzón-Agudelo & Kevin Epperly, we used 2D & 3D shape data to show:
Beaks are getting more slender, tapered, and in males, pointier! 🐦
nicmalexandre.bsky.social
Co-first author Faye Romero and I modelled bill changes of Anna’s hummingbirds in the Museum of Vertebrate Zoology’s collection (dating to 1860). 📏
We found bill length and maxillary surface area increased with feeder density.
nicmalexandre.bsky.social
Building on that, co-first author Simon English showed that feeder abundance was the best predictor of Anna’s hummingbird population growth, especially in the north, where Grieg et al. showed that birds rely more on feeders.
nicmalexandre.bsky.social
It started with newspaper archives 📜:
Prof. Eliza Grames tracked hummingbird feeder mentions by county in California from 1860 on. She found feeder use rose rapidly, especially from southern to northern CA.
nicmalexandre.bsky.social
The starry sturgeon (A. stellatus) carries extra Hox genes, genes that control body plans, but not all are active! After genome duplications, some genes turned off, while others evolved new functions. #2025MMM #RIP
Schematic illustration of the sterlet hox complement. Eighty eight hox genes were identified plus one pseudogenized hoxd14 gene (indicated by psi). All hox clusters are retained in duplicate. B. Reconstruction of the ancestral actinopterygian condition and the inference of gene losses across the gnathostome phylogeny on the basis of the sterlet pretetraploidization hox complement in combination with that of the gar. The inferred ancestral Hox complements are shown in purple (likewise indicated by the purple arrowhead in the tree) for gnathostomes, in blue for Sarcopterygii and in orange for Actinopterygii.
nicmalexandre.bsky.social
Gemmel et al sequence the Tuatara genome in 2020 and found the lineage diverged from snakes and lizards 250 Mya. The tuatara genome is 2.4× larger than the anole genome but 64% of it is repetitive sequences and has the highest
percentage of methylation for an amniote #2025MMM doi.org/10.1038/s415...
An image of a Tuatara now only found in Aotearoa. A map of Rhincocephalia fossil sites showing a global distribution. Phylogenetic tree of amniotes placing Tuataras at the base of Lepidosaurans.
nicmalexandre.bsky.social
Sturgeons have undergone multiple whole-genome duplications, making some species octoploid (8x their original genome)! A. stellatus is a “low-ploidy” sturgeon, but its DNA still carries echoes of ancient duplications. #2025MMM doi.org/10.1038/s415...
Species tree built on the basis of 47 one-to-one orthologues. Red stars indicate whole genome duplications after the first and second duplication event.
nicmalexandre.bsky.social
The genomes of arbuscular mycorrhizal (AM) fungi reveal they have lost some metabolic pathways relative to free-living fungi. Kobayashi et al 2018 find that thiamine, vitamin B6, and some glucose-producing polysaccharide hydrolases biosynthesis is absent in AM #2025MMM #RIP doi.org/10.1186/s128...
Glucose-producing hydrolases of AM fungi and other fungi. Enzymes present in organisms are indicated by colored backgrounds. Out of seven  metabolic pathways, AM Fungi only had genes for two.
nicmalexandre.bsky.social
Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Morin et al 2019 find that AM genomes contain a lot more species-specific genes than other fungi, which reflects their unique lifestyle #2025MMM doi.org/10.1111/nph....
Mycorrhizal fungi have a large number of unique genes relative to non-mycorrhizal fungal species. (a) Organismal phylogeny. (b) Bar graphs representing sets of conserved proteins shared among species (dark blue), sets of duplicated conserved proteins shared among species (light blue), sets of dispensable proteins (purple), sets of duplicated dispensable proteins (light purple), and species-specific (orange) and duplicated specific-specific (light orange) proteins. Note that some of the species-specific genes found by comparing the eight Mucoromycota genomes have orthologues in other fungi (yellow).
nicmalexandre.bsky.social
Zhao et al in 2019 sequenced 545 genomes of ginkgos and found 3 centers of genetic diversity in China. Ginkgos grown outside China trace their ancestry to the East population, and American and European trees carry genetic variation that is rare in wild populations. doi.org/10.1038/s414... #2025MMM
Phylogenetic relationships and population structure of 545 ginkgo samples around the world.  a Geographic distribution of the sampling locations.  b Model-based population assignment by ADMIXTURE analysis for K = 2–5. c Principal component analysis (PCA) of Chinese samples, with the proportion of the variance explained being 8.61% for PC1 and 6.18% for PC2. d A neighbor-joining (NJ) phylogenetic tree of all 545 ginkgo samples around the world constructed using whole-genome SNP data based on pairwise identity-by-state (IBS) genetic distances.
nicmalexandre.bsky.social
A fern genome contains all the instructions for two independent multi-cellular phases: a gametophyte (prothallus) and a sporophyte (fern). Yet, Marchant et al 2023 find only 273 and 1,397 genes were specifically expressed in the gametophyte and sporophyte #2025MMM #RIP doi.org/10.1038/s414...
A single fern genome contains all the genetic instructions for two different and independent multi-cellular phases, a gametophyte (prothallus) and a sporophyte (adult fern). Ferns do this by expressing different genes during each phase, this Vinn diagram shows how for Ceratopteris 273 genes are expressed only in the gametophyte, 1397 genes are expressed only in the sporophyte and 33028 are expressed in both.
nicmalexandre.bsky.social
Ferns are the second most species-rich lineage of land plants. Fujiwara et al 2023 found that fern genome sizes have grown as fern have diversified, showing large structural complexity between different fern species due to whole genome duplications and polyploidy #2025MMM doi.org/10.1093/aob/...
This scatterplot shows the correlation between holoploid genome size (1C) and gametic chromosome number (n) (A) and the correlation between monoploid genome size (1Cx) and basic chromosome number (x)