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Reposted by Nicolas Alexandre

Christopher Witt @msbbirds.bsky.social · 28/05/2025

New paper on ecosystem-wide PFAS contamination at Holloman AFB, New Mexico authors.elsevier.com/c/1lAOb3Ao6B...

Winter evening at Holloman Lake, New Mexico

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Reposted by Nicolas Alexandre

Lizzy Steell @lizzysteell.bsky.social · 23/05/2025

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/...

onlinelibrary.wiley.com

Fitting the Bill in an Urban World: Hummingbird Beak Shape Responds to Anthropogenic Factors

Click on the article title to read more.

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Nicolas Alexandre @nicmalexandre.bsky.social · 21/05/2025

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...

science.org

Bird feeders have caused a dramatic evolution of California hummingbirds

Beaks have grown longer and larger, and ranges have expanded to follow the feeders

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Nicolas Alexandre @nicmalexandre.bsky.social · 14/03/2025

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.

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Nicolas Alexandre @nicmalexandre.bsky.social · 14/03/2025

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.

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Nicolas Alexandre @nicmalexandre.bsky.social · 14/03/2025

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.

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Nicolas Alexandre @nicmalexandre.bsky.social · 14/03/2025

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.

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Nicolas Alexandre @nicmalexandre.bsky.social · 14/03/2025

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).

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Nicolas Alexandre @nicmalexandre.bsky.social · 14/03/2025

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.

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Nicolas Alexandre @nicmalexandre.bsky.social · 14/03/2025

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.

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Nicolas Alexandre @nicmalexandre.bsky.social · 14/03/2025

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)

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Nicolas Alexandre @nicmalexandre.bsky.social · 14/03/2025

The frilled shark (Chlamydoselachus anguineus) has barely changed for 80 million years! 🦈 Its DNA reveals it's one of the most ancient sharks, diverging before most modern species existed. A true relic of deep-sea evolution! 🌊 #2025MMM doi.org/10.1155/2013...

Maximum likelihood phylogeny depicting relationships among 19 Chondrichthyes species inferred from the whole-mtDNA sequences. Numbers on the branches are bootstrap support values.

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