Endless Tigers Most Beautiful

The Thylacine, or the Tasmanian Tiger, is a tragic story that we all know (or should know!). Too late did humans realize how precious it was, a large(ish) marsupial carnivore endemic to Tasmania. Hunted to extinction, the last one died because it was not properly taken care of.

The Tasmanian Tiger is an example of why science is not just instrumental. That is, science is not simply the handmaid of engineering. Most people with an interest in biology have some instinctive reaction to the Tasmanian Tiger and what happened. There’s a natural pathos in it.

If you read The Monkey’s Voyage you know that the marsupials of South America probably derive from a single dispersal event. Genetics has determined that the South American Monito del monte is the most basal of the superorder Australidelphia, which includes all Australasian marsupials. That means instead of the single South American marsupial of this superorder being due to a migration from Australia, the Australian lineages diversified from a single South American ancestor. The Monito del monte is the last living descendent of this once extensive clade.

This means that all of the vareigated marsupials of Australia probably diversified during the Cenozoic, even though the divergence between marsupials and placental mammals dates deep into the Mesozoic. The Koala, the Kangaro, and the Tasmania Devil, all derive from the same source.

Well, a new paper in Nature: Ecology & Evolution does something quite neat, they sequence the whole genome of a Tasmanian Tiger! Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore:

The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.

The authors are saying that the clear morphological convergences between Tasmania Tigers and canids, which are obvious to anyone with eyes, aren’t detectable in similar sequence identity in regions of the genome known to be functional relevant to the characteristics of interest. Instead of sequence identity they suggest that rather the morphology is being controlled by evoutionary genetic process of cis-regulatory adaptation.

In the Mike Lynch vs. Sean Carroll debate of about ten years back, they’re saying that Sean Carroll was right (see this Hoekstra & Coyne paper for a different take).

Part of the issue here is probably the sort of traits they’re focused on. There seems to be something about the gross morphological characteristics humans find salient that make them the target of cis-regulatory mediated evolutionary processes.

Finally, they suggest with a PSMC plot that Tasmanian Tiger populations crashed around 70,000 years ago, well before Australian Aboriginals arrived. First, I’m not sure that I trust the 70,000 number to be precise enough that we can say it doesn’t overalp with human arrival. But second, is it me, or does every PSMC look like the pot above? It’s probably some sort of publication bias, as you don’t put in PSMC figures if they don’t show a bottleneck. But I’m kind of getting tired of it.