Moritz Blumer

Three cichlid fish swimming in clear water, with text at the bottom asking 'How do 'supergenes' shape the evolution of fish?'

How did nature’s incredible diversity come to be? These cichlid fish may offer a clue 🐠

Cambridge researchers have found that chunks of ‘flipped’ #DNA can help fish quickly adapt to new habitats and evolve into new species, acting as evolutionary ‘superchargers’ 👇
bit.ly/3HGqEN6

And thanks to all other co-authors, some are on bluesky:
@currocam.bsky.social
@alexhooft.bsky.social
@joelelkin.bsky.social
@millanek.bsky.social
@dlimnothrissa.bsky.social
@domino-joyce.fishsci.com.ap.brid.gy
@astridboehne.bsky.social
@emiliapsantos.bsky.social
@ericmiska.bsky.social

A special thanks to everyone involved in this long-term project, especially the main authors Valentina Burskaia, Ilia Artiushin, @sahajaysmita.bsky.social, Hannes Svardal and Richard Durbin. Stay tuned for more interesting inversion stories!

Taken together, our findings point towards a dual role for recombination-suppressed regions (in our case: inversions) in the evolution of cichlid adaptive radiations. This is in line with another very nice recent study (Kumar et al., doi.org/10.7554/eLife.104923.2) who found the same inversions.

(As a side note: We also found evidence that previously identified sex determination systems in the Lake Victoria sister radiation are most likely inversions, but emerged independent from the Malawi ones).

Interestingly, we found strong evidence that at least three inversions are involved in sex determination in some lineages, while the same inversions do not determine sex in other groups.

Together with the origin of two inversions in the deepwater 𝐷𝑖𝑝𝑙𝑜𝑡𝑎𝑥𝑜𝑑𝑜𝑛 lineage, and the higher inversion frequencies in the extant deep clade, we believe that these inversions played a role when lineages adapted to different habitat depths, one of the most common axes of diversification in fish.

Focusing on the SNPs from within the inversion regions that were most correlated with inversion state, we identified patterns of positive selection that were enriched for genes related to sensory perception.

Interestingly, we found evidence that uninverted haplotypes of these inversions in benthics introgressed repeatedly from riverine lineages, in one case likely even from a 𝑃𝑠𝑒𝑢𝑑𝑜𝑐𝑟𝑒𝑛𝑖𝑙𝑎𝑏𝑟𝑢𝑠-like outgroup to the Malawi radiation, a lineage that still exists in the surrounding rivers today.

In particular, the chromosome 9 and the compound chromosome 11 inversions likely arose in the proto 𝐷𝑖𝑝𝑙𝑜𝑡𝑎𝑥𝑜𝑑𝑜𝑛 lineage and remain polymorphic among today’s benthics.

... we believe that the most species rich and ecologically diverse subradiation arose from a hybridization event between the ancestors of two ecologically contrasting lineages: the riverine-like 𝐴. 𝑐𝑎𝑙𝑙𝑖𝑝𝑡𝑒𝑟𝑎 and the deepwater specialists 𝐷𝑖𝑝𝑙𝑜𝑡𝑎𝑥𝑜𝑑𝑜𝑛.

Taking into account all available lines of evidence, especially the phylogenetic distribution of the inversions (see the first image) and patterns of allele sharing among Malawi clades and outgroups within and outside inversion regions ...

Using new chromosome-level assemblies and haplotagged (linked) reads of representatives of the major clades we confirmed that these regions are in fact inversions. Pairwise alignments also showed that the outlier region on chromosome 11 consists of two adjacent but co-segregating inversions.

Using windowed PCA and a new clustering approach we identified five chromosome-scale regions with aberrant phylogenetic patterns – consistent with large and divergent segregating haplotypes.

The biallellic variant callset is available for download: doi.org/10.17863/CAM....

Following a decade of field work with many collaborators from Europe and Malawi, we sequenced 1,375 Malawi cichlids from 240 species (covering all major ecomorphological clades) and called variants against a chromosome-level 𝐴. 𝑐𝑎𝑙𝑙𝑖𝑝𝑡𝑒𝑟𝑎 reference genome.

A circular phylogeny of Malawi cichlids with inversion frequencies indicated for different taxa as rings around the tree.

Check out our new paper about chromosomal inversions in Malawi cichlids! 🐟🧬

Available here without a paywall: hdl.handle.net/10067/214834... (click on the ‘Full text (open access)’ link).

Various Malawi cichlids in the shallow waters of Otter Point, Malawi

‪🐟 How do new #species arise?🧬 800+ species, 1 lake, little time: Cichlids in Lake #Malawi evolved with stunning speed—no geographic barriers needed. A new Science study shows how #supergenes & chromosome inversions drive biodiversity. #LIBresearch
Find out more: leibniz-lib.de/de/news/1206...

@fxquah.bsky.social 's paper is finally out @genomeresearch.bsky.social and we made the cover!! This was only possible due to the brilliant illustration by @sonhita.bsky.social

Paper here:
genome.cshlp.org/content/35/5...

See below for more details 🧵

Dass ausgerechnet die CSU-Politikerin Doro Bär, die noch vor wenigen Jahren den menschengemachten Klimawandel leugnete, jetzt neue Forschungsministerin werden soll - ein Job, bei dem es ganz besonders darauf ankommt, der Kraft der Wissenschaft zu vertrauen, ist m.E. hochproblematisch.

Dire Wolves Were Not Really Wolves, New Genetic Clues Reveal The extinct giant canids were a remarkable example of convergent evolution

Dire wolves were not close relatives of gray wolves. They last shared a common ancestor more than 5 million years ago. What Colossal has done is make something new and slapped a dire wolf sticker on it, as if an organism equals a hypothetical genome.

Do you want to make genetic maps from sperm/pollen/gametes? Now there is an easy way, based on Hi-C sequencing.

Thanks to Richard Durbin and Ed Green for the idea and a group of co-authors including @mariontalbi.bsky.social and @danielbolnick.bsky.social for contributions.

Germans have been subjected to covert Russian propaganda as well as overt American propaganda - jointly in support of the far-right
www.nytimes.com/2025/02/13/w...

Airbnb’s co-founder is joining Elon Musk’s DOGE Gebbia, a close friend of Musk, has praised DOGE’s work and defended it against criticisms on social media

Time to evict AirBnB from your life, if you have't already.

Welcome to Trump Tracker: Probationary workers at health agencies being fired today Follow President Donald Trump’s impact on U.S. research and science globally

There is a lot going on right now! So much in fact that our news team at @science.org is now running a Trump tracker to keep track of it all. *sigh* 🧪

www.science.org/content/arti...

'It’s tectonic:’ U.S. foreign aid freeze deals a blow to research around the globe Dismantling of USAID could disrupt many clinical trials and wipe away U.S. “soft power” in developing countries, scientists warn

The dismantling of USAID could disrupt many clinical trials and wipe away U.S. “soft power” in developing countries, scientists warn.

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes - Genome Biology Background East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable e...

Our first deep dive into TEs and piRNAs in African cichlids is finally published!

genomebiology.biomedcentral.com/articles/10....

rdcu.be/d69S5

Our main findings below 🧵

#TEsky

Bat genomes illuminate adaptations to viral tolerance and disease resistance - Nature A systematic analysis of 115 mammalian genomes, including 10 new bat genomes, reveals prevalent positive selection in immune genes in bats and shows key adaptations in the antiviral gene ISG15 that ai...

Happy to report that our work on immune system adaptations in bats is now out in @nature.com 🦇🧬 www.nature.com/articles/s41... @ariadnamorales.bsky.social @batresearch.bsky.social @virology.bsky.social @DGKontopoulos.ecoevo.social.ap.brid.gy @sgn.one @bat1kgenomes.bsky.social Read more ...