Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II

Type: Journal article

Reference: Luke W Silver, Carolyn J Hogg, Katherine Belov, Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II, Genome Biology and Evolution, Volume 16, Issue 8, August 2024, evae156, https://doi.org/10.1093/gbe/evae156

Abstract

The major histocompatibility complex (MHC) plays a vital role in the vertebrate immune system due to its role in infection, disease and autoimmunity, or recognition of “self”. The marsupial MHC class II genes show divergence from eutherian MHC class II genes and are a unique taxon of therian mammals that give birth to altricial and immunologically naive young providing an opportune study system for investigating evolution of the immune system. Additionally, the MHC in marsupials has been implicated in disease associations, including susceptibility to Chlamydia pecorum infection in koalas. Due to the complexity of the gene family, automated annotation is not possible so here we manually annotate 384 class II MHC genes in 29 marsupial species. We find losses of key components of the marsupial MHC repertoire in the Dasyuromorphia order and the Pseudochiridae family. We perform PGLS analysis to show the gene losses we find are true gene losses and not artifacts of unresolved genome assembly. We investigate the associations between the number of loci and life history traits, including lifespan and reproductive output in lineages of marsupials and hypothesize that gene loss may be linked to the energetic cost and tradeoffs associated with pregnancy and reproduction. We found support for litter size being a significant predictor of the number of DBA and DBB loci, indicating a tradeoff between the energetic requirements of immunity and reproduction. Additionally, we highlight the increased susceptibility of Dasyuridae species to neoplasia and a potential link to MHC gene loss. Finally, these annotations provide a valuable resource to the immunogenetics research community to move forward and further investigate diversity in MHC genes in marsupials.

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When Cells Rebel: the dark side of evolution

by Patra Petrohilos (PhD Student)

I love dystopian horror. I love to relish in the thrill of disgust from the comfort of safety – a comfort bolstered by the knowledge that such grotesquerie could never actually happen in real life. Zombies don’t exist. Monsters aren’t trying to escape from the underworld. Cancer isn’t contagious. Actually, maybe scratch that last one. . .

You see, nature may not have the imagination of Stephen King, but it does have something even more powerful in its arsenal: mutations. Mutations are to evolution what creativity is to horror writers – the raw material that allows them to conjure up new and wondrous forms. From the most beautiful (buttercups, butterflies, butter yellow bumblebees) to the most horrific (flesh eating bacteria, pandemic inducing viruses, cancer cells).

Evolution favours the fittest individuals, be they butterflies or bacteria. In this case, “the fittest” just means the ones that are most successful at reproducing. If we are talking about koalas, reproduction means making cute little baby koalas. Everyone likes those. But when we’re talking about cancer cells, reproduction means growing and spreading and killing one’s host. Nobody likes that. Even the cancer cells probably wouldn’t like it – because killing their host also means killing themselves in the process. Kind of like a suicide bomber without the political motivation. But evolution is blind to morality and selects for the cute little baby koalas and murderous cancer cells equally – whatever is most efficient at making more copies of itself. Survival of the fittest.

Mutations are constantly arising in nature. Sometimes these make more successful versions of things, sometimes less successful. It’s a bit of a trial-and-error process. And somewhere in that trial-and-error process, a handful of cells have stumbled across the secret to become the most successful cancer cells ever. Super-cancers! How? By finding a sneaky way around that whole unfortunate dying-when-your-host-dies bit.

They do this by taking a leaf out of the life history book of parasites. Like cancer cells, many parasites are reliant on a host to survive. But unlike cancer cells, many parasites have the power to survive the death of their host by simply finding a new host – a power that evolution has also bestowed upon these super-cancers.

Yes, nature has managed to take one of the most awful diseases known to humanity and done perhaps the only thing that could make it worse. It has made it contagious.

Thankfully, such contagious super-cancers are mercifully rare and none of them affect humans (yet). But the rest of the animal kingdom has not fared quite so well. Leukaemia cells drift through the sea like hidden assassins, spreading from one unsuspecting clam to the next. Dogs can get mushroom shaped tumours on their penises from sex with a poorly chosen partner. And one of our most iconic Australian animals, the Tasmanian devil, is at risk of extinction from not only one but two contagious cancers (creatively named Devil Facial Tumour Disease 1 and Devil Facial Tumour Disease 2). Sometimes lightning really does strike twice.

The good news is, this is where we come in. By researching Devil Facial Tumour Disease – one of the most uniquely horrifying and bizarre diseases to ever arise – we aim to understand how it works, how it spreads, how it evolves and, hopefully one day, how we can stop it.

Follow me for more fun and uplifting facts about the animal world!

Author:

Patra Petrohilos

Patra Petrohilos (PhD Student) is researching the evolution of devil facial tumour disease (DFTD). By investigating anticancer properties of naturally occurring peptides, she is aiming to identify novel agents with therapeutic potential against DFTD. Patra Petrohilos is a PhD student with the Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science (CIPPS). Follow their exciting research at https://cipps.org.au.

Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates

Type: Journal article

Reference: Toby G L Kovacs, James Walker, Simon Hellemans, Thomas Bourguignon, Nikolai J Tatarnic, Jane M McRae, Simon Y W Ho, Nathan Lo, Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates, Systematic Biology, Volume 73, Issue 3, May 2024, Pages 532–545, https://doi.org/10.1093/sysbio/syae002

Abstract

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analyzed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by phylogenetic analyses of mitochondrial genomes and UCE loci. Furthermore, Bayesian dating analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all 13 major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.