Glad to see our work @tjnear.bsky.social being covered in Nature! I look forward to both preprints being published, and I want to add that it appears genomes AGREE with morphology, and REFUTE the mtDNA-based hypothesis that was controversial when it first appeared!
www.nature.com/articles/d41...
40-44 (GOP combined) in MTG's seat. Republicans are COOKED in November god DAYUM
10/10 Thanks to Yale University & the Peabody Museum
for support as always, and to our lab and department for helpful discussions!
9/10 These results highlight how, even in a period when genomes and phylogenies are becoming available for all orders of biodiversity, major questions remain about the relationships of some of the most iconic and threatened animal lineages!
8/10 Based on the results of these phylogenomic analyses, we suggest that sharks and rays ancestrally underwent a single major genome size increase as long ago as the Permian. Sharks have had massive genomes for nearly 300 million years!
7/10 By using genomic data to calibrate this phylogeny in time, we also demonstrate that sharks and rays participated in the Mesozoic Marine Revolution, a major period of diversification in the oceans that lasted from between 200 and 100 million years ago.
6/10 Regardless of whether sharks form a clade exclusive of rays, we still can reach consensus around key aspects of their evolutionary history, such as the origins of live birth and pelagic specialization!
5/10 We highlight the monophyly of sharks as a major remaining issue in vertebrate and animal phylogenetics. This issue is also of conservation importance, since it would impact the estimated evolutionary distinctiveness of many species! (Photo: Stein et al., 2018 Nature EE)
4/10 This controversy hinges on the position of the Hexanchiformes, which include the sixgill and frilled sharks! These bizarre species share some aspects of their anatomy with sharks that existed before the dinosaurs!
3/10 We discovered that sing different types of commonly used genome-wide markers, such as UCEs and BUSCO genes, produce fundamentally different hypotheses about shark and ray evolution! Depending on the type used, sharks are NOT necessarily their own clade!
2/10 As it happens, the relationships of sharks, skates, rays, and chimaeras, which compose the cartilaginous vertebrates, are historically contentious. I wanted to see what we could do with genome sequences, and Tom and I went to work!
1/10 ⏰⏰ New stuff from me &
@tjnear.bsky.social
! We show that sharks themselves might not be a natural group ... it depends on what spots in the genome you analyze!
Preprint here: www.biorxiv.org/content/10.6...
16/16 Finally, thanks to @lifesciencestudios.bsky.social for the watercolors! I want to say finally that this type of interdisciplinary work is not possible at all without federal funding. Please #standupforscience
15/16 Thanks, as always, to my coauthors, including co-first author Maxime Policarpo, my advisor @tjnear.bsky.social and Richard Harrington, Eva Hoffman, Maya Stokes, and Didier Casane! Thanks as well to the Yale Peabody Museum, Yale EEB and TPG TPG for support!
14/16 The ages of the cave-related vision gene loss logically postdate the caves, so the ages we get are the minimum ages of the subterranean ecosystems! This suggests that some of these cave systems are up to 15 million years old! These systems have been here since the Miocene!
13/16 But we can go further! What about the caves themselves? The ages of eastern North America's iconic karst caves, such as Mammoth Cave, are actually really hard to date using conventional methods. Cavefishes fill the gap! (Photo: NPS)
12/16 Well, most anyways. Some, like species in the genera Amblyopsis and Typhlichthys, actually have pseudogene ages that predate their divergence from other species in each genus! Thus, these genomic markers of cave adaptation came before-these fishes speciated underground!
11/16 As it turns out, the ages we get from examining this pseudogene clock are younger than the divergence times of cavefish lineages from one another! So, they experienced cave-associated degenerative evolution AFTER diverging from other fishes, and thus independently!
10/16 To get to the bottom of this, we used a trick. By estimating generation times since a gene was pseudogenized, and then multiplying that by years per generation, we can estimate how many millions of years ago a cavefish, well, became a cavefish!
9/16 The problem is that, for single species diverging from a surface-dwelling ancestor, cave colonization and adaptation could have happened anywhere along the branch on the tree leading to the living cave dweller. This is because its closest surface relatives might be extinct!
8/16 We noticed that the number of pseudogenes might be associated with the age of cave lineages themselves. For example, Troglichthys rosae, the first obligate cave-dweller to diverge, pseudogenized 25 vision and light related genes ancestrally!
7/16 What's more, no loss of function mutations appear ancestral to lineages including multiple obligate cave-dwelling amblyopsid genera, nor are none present in Forbesichthys! This indicates independent cave colonization and subsequent gene function loss. But there's more!
6/16 Different sets of vision-related genes, including several involved in human disease, lost functionality in different lineages of obligate cave-dwelling amblyopsids! Not only that, but the loss of function mutations themselves are not identical among lineages!
5/16 Although the similarities of obligate cave-dwelling amblyopsids are not just skin deep (they have all elongated their skulls and bodies, deossified their circumorbital series, and reduced or lost pelvic fins), comparisons of their genomes show these fishes are convergent!
4/16 A clue is that eyed, pigmented species in Forbesichthys are deeply nested within blind, obligate cave dwelling amblyopsids, suggesting multiple origins. By using genomes, personal examination of key fossils, and CT scans, we built the most comprehensive tree yet to do so!
3/16 Most amblyopsids have degenerated their eyes and lost external pigment to become obligate cave-dwellers. Yet, the different ways in which the eyes of different species have degenerated has led to a 125-year debate about how many times these fishes invaded caves! (Photo: NPS)
2/16 Amblyopsids are one of North America's most obscure and most interesting vertebrate lineages. Endemic to eastern North America, they are part of a species-poor lineage that also includes pirate and trout perches and originated 80 million years ago!
1/16 🚨🚨 New paper!! I am thrilled to share our study that uses fossils, genomes, and a bit of geology to investigate how many times cavefishes evolved, and how they can help us figure out the ages of caves themselves! Link: academic.oup.com/mbe/advance-...
Checking genbank for an obscure clade
