Incomplete lineage sorting impacted the evolution of marsupials

This evolutionary process shaped the morphological patterns among these animals.

On the Avian Hybrids blog, I often write about introgression, the exchange of genetic material through hybridization and backcrossing. This phenomenon can be detected with numerous methods (which I covered in this review), including the observation that some gene trees deviate from the species tree. When a gene is transferred from one species to another, it is logical that its trajectory might deviate from the main evolutionary history. However, a discordant gene tree does not automatically imply introgression. Other evolutionary processes can produce similar patterns. A recent study in the journal Cell took a closer look at one of these processes: incomplete lineage sorting.

ILS and M&Ms

I have always found incomplete lineage sorting (or ILS) a difficult concept to grasp. In essence, it refers to the sorting of genetic variation from an ancestral population into several descendant lineages. An analogy might be helpful. Consider a big jar of differently colored M&Ms (i.e. the ancestral population with genetic variants). If you would randomly divide these colorful candies into four small jars (i.e. the descendant lineages), you can expect that these jars will share some colors. You will likely not end up with one color per jar. The bigger the ancestral jar, the less likely that the candies will be completely sorted per color in the small jars. Over time, the contents of the small jars might become homogenized through the removal of certain colors (either randomly or by a selected eater that might prefer certain colors). At some point, you might end up with nicely color-sorted M&M-jars. Obviously, this analogy is not perfect but I hope you get the general idea. ILS is the random distribution of ancestral variation into descendant lineages.

A graphical illustration of incomplete lineage sorting. An ancestral population with several genetic variants (differently colored dots) splits into three descendant lineages. Right after each split, you can see that the lineages share genetic variants (this is ILS). Over time, some variants disappear – randomly or through selection – resulting in completely sorted lineages of one color. From: The Coop Lab.

Sister Species

Now that we have a good understanding of ILS, we can dive into the paper which focused on the evolution of marsupials. I am aware that marsupials are not birds, but the methods and findings of this study were so cool that I could not let it slide. There is more to life than avian hybrids. In the study, the researchers focused on the phylogenetic position of the Monito del Monte (Dromiciops gliroides). It is unclear whether this South American species is most closely related to the Diprotodontia (e.g., the Koala, Phascolarctos cinereus) or the Dasyuromorphia (e.g., the Tasmanian Devil, Sarcophilus harrissii). Some studies have found that the Monito del Monte is the sister species to these two clades, while other studies placed it within one of the two groups. Using whole genome sequences, Shaohong Feng and colleagues provided some clarity in this evolutionary mystery and presented convincing evidence that the Monito del Monte is indeed the sister species to the two Australian groups.

Whole genome analyses revealed that the Monito del Monte is the sister species to the Australian marsupials in the clades Diprotodontia and Dasyuromorphia. From: Feng et al. (2022).

Divergence Times

Next, the researchers quantified the level of gene tree discordance (i.e. the number of gene trees deviating from the species tree). They found that more than 50% of the investigated genes did not follow the evolutionary pattern of the species tree. In about 30% of the cases, the Monito del Monte clustered with the Diprotodontia. And roughly 28% of the gene trees combined the Monito del Monte with the Dasyuromorphia. To determine whether these patterns are due to ILS or hybridization, the researchers performed a suite of additional analyses. I will focus on one particularly interesting approach: comparing divergence times of gene trees. Hybridization occurs when speciation has already started whereas ILS can be traced back to the ancestral population. Hence, deviating gene trees with older divergence times point to ILS. And indeed, the researchers noted:

Our analyses confirmed that the ILS regions had an older divergence time between monito del monte and the Dasyuromorphia (52.3 mya) or the Diprotodontia (54.0 mya) than the genomic regions that corresponded with the actual species differentiation (45.8 mya). Moreover, the biogeographic data show that the final separation of Australia and Antarctica along the South Tasman Rise occurred at ca. 45 mya, i.e., at the time that early diversification of the Australian marsupials began according to our estimation.

This results was corroborated by several other analyses, such as D-statistics, quantifying introgression via branch lengths (QuIBL) and coalescent hidden Markov models (CoalHMM). I will not dive into the details of these methods. The main message is that ILS has been a dominant force in the evolution of marsupials.

Transgenic Mice

The finding that ILS has played such a big role during the radiation of marsupials is definitely interesting, but the best part of the study is yet to come. Numerous studies have documented ILS, but few have explored the consequences of this process. In the Cell-paper, the researchers did go one step further. They identified several genes that have been impacted by ILS and determined the morphological effects of these genes. Using experiments with transgenic mice.

The gene WFIKKN1, for example, is involved in the development of vertebrae. The Monito del Monte and the Koala carry one version of this gene (with a glutamine at position 76), whereas the Tasmanian Devil has another version (with am arginine). These species also differ the structure of the spinous process, which is a bony projection off the back of each vertebra. In the Monito del Monte and the Koala, the first spinous process on the vertebra is quite long. In the Tasmanian Devil, however, the first spinous process is significantly shorter. When the researchers introduced the Tasmanian Devil-variant in transgenic mice, they observed a decrease in the spinous process. Direct evidence of the morphological effect of this gene!

Genetic variants of the WFIKKN1-gene (indicated in the blue box) impact the structure of vertebrae. Species with a glumatine (Q) develop a long spinous projection, while species with a arginine (R) show a reduction. This effect was also observed in transgenic mice. From: Feng et al. (2022).

Trait Evolution

What does this all mean? The observation that ILS can create similar morphologies in distantly related species forces us to partly rethink how evolution works. These morphological similarities are generally explained as the result of convergent evolution. Distantly related species have independently evolved the same phenotype, probably driven by different genetic changes. When ILS is involved, this picture changes. The morphological similarities can be traced back to the same genetic changes that were present in the distant ancestors of these species. These traits did not arise multiple times independently, but originated once and were then distributed across distinct descendant lineages. A subtle but crucial difference. The observation that not all morphological similarities between distantly related species are the outcome of convergent evolution has important implications for (macro)evolutionary analyses. Moreover, considering that introgression can also transfer traits across the evolutionary tree (e.g., the white coat of snowshoe hares), it is clear that reconstructing the evolutionary history of a trait is no easy feat.

References

Feng, S., Bai, M., Rivas-Gonz├ílez, I., Li, C., Liu, S., Tong, Y., … & Zhang, G. (2022). Incomplete lineage sorting and phenotypic evolution in marsupials. Cell.

Featured image: graphical abstract of the study.