Posts Tagged ‘paleogenetics’

Research Publication Title of the Week – The Virtue of Modesty

26 May 2009
Comparison of the five extant species of rhinoceros - Wikimedia Commons

Comparison of the five extant species of rhinoceros - Wikimedia Commons

ANALYSIS OF COMPLETE MITOCHONDRIAL GENOMES FROM EXTINCT AND EXTANT RHINOCEROSES REVEALS LACK OF PHYLOGENETIC RESOLUTION – Eske Willerslev, Marcus Gilbert, Jonas Binladen, Simon Ho, Paula Campos, Aakrosh Ratan, Lynn Tomsho, Rute da Fonseca, Andrei Sher, Tatanya Kuznetsova, Malgosia Nowak-Kemp, Terri Roth, Webb Miller  and Stephan Schuster

BMC Evolutionary Biology 2009, 9:95

doi:10.1186/1471-2148-9-95

From our irregular series - Bloggers half-assedly opining about peer-reviewed papers when, really no one asked them in the first place anyway

From our irregular series, oh, nevermind.

Amidst the recent outcry over phylogenetic hype, it is nice to see some truth in advertising.  Sure one might quibble over whether the lack of a pattern is something that can be “revealed” but microecos never quibbles over semantics…

Semantics aside, what is tremendously cool about this paper is the recovery of mitochondrial genes from preserved soft tissues of the extinct woolly rhino, Coelodonta antiquitatis. Despite the overall lack of resolution among the clade, Willerslev and company recover strongly supported sister relationships between the two African rhinos (the white rhino, Ceratotherium simum and the black rhino, Diceros bicornis) and between the congeneric Javan and Indian rhinos (Rhinoceros sondaicus, R. unicornis).

Charles Knights famous, heroic woolly rhino

Charles Knight's iconic, heroic woolly rhino

While neither of these relationships are surprising, the authors also found support for a sister relationship between the woolly rhino and the ridiculously adorable, critically endangered Sumatran rhino (Dicerorhinus sumatrensis).  This relationship has been postulated before, at least partly based on the fact that Dicerorhinus is unique among living rhinos in sporting luscious, auburn locks that put agent Scully to shame.  However, this hypothesis has been controversial and this new paper certainly leaves the door open for considerable improvement in our understanding of the evolutionary history of living rhinos.

One of the problems here is that today we are left with only a tattered remnant of the great perissodactyl radiation that produced some of the most impressive, perplexing and yes (ahem) EXTREME mammals that have ever existed.  Aside from the four rhino genera, a handful of tapirs (all in genus Tapirus) and a rather more respectable smattering of zebras, asses and kiangs (in the familiar, but rather lumpy genus Equus) are all that remains of this once diverse order.  In the recent analysis, relationships amongst the rhino couplets changed dramatically depending on whether tapirs or horses were used as the out-group, perhaps indicating a geologically explosive radiation of rhinos from their perissodactyl ancestors at some point in the Cenzoic.

Living rhinos on the brink - from http://www.rhinos-irf.org/rhinosincrisis/

Living rhinos on the brink - from Intl Rhino Foundation

Sadly, we stand to lose even more of this evolutionary majesty if the poaching and deforestation that imperil all living rhinos isn’t checked.  While the recovery of genetic material from the extinct woolly rhino is a remarkable achievement, it would be terribly tragic if scraps of keratin are all that future studies of rhino evolution have to go on.

But I hate to leave you on such a bitter note, so behold, the otherworldly wonder that is a baby Sumatran rhino:

Baby Rhino!

Baby Rhino!

Genomics and the Incognitum

16 August 2007

Four blind wisemen are examining a skull. The first grasps the tip of the tusk and shouts “it’s a spear!” The second feels the deep concave nasal cavity at the center of the skull and exclaims “no, it’s a cyclops, to be sure!” The third rubs the jagged molar and muses, “cyclopses don’t exist, but surely this was a fearsome carnivore.”

Then the fourth wiseman walks up and lightly taps the tip of the occipital condyle he probes the foramen magnum. Then he draws his finger up and across the low-domed skull and explores the depths of the nasal cavity. He carefully strokes each long conic incisor before moving deeper into jaw.  He traces each cusp and groove along each tooth. After some time, the fourth scientist quietly states, “It’s a proboscidean, specifically an American Mastodon (Mammut americanum) or something like it.”

LOL! Genomics takes the old fable of the blind man and the elephant to heart. Rather than studying genetic information by examining minute bits (like only 10,000 base-pairs or something), or ‘genes’ the genomicists examine entire organimsal genomes, the forest rather than the trees if you’d like (alt. getting complete sets is no mean feat, even from a living organism.

That makes the announcement of the sequencing of an entire Mastodon mitochondrial genome from a tooth wrenched from the Alaskan permafrost totally effing astonishing. And really, really cool. Even better it’s been published in PLoS and is free for all to ponder, ruminate and expound upon.

One application of whole-genome studies is evolutionary comparison between related organisms. In this case, the researchers compared the Mastodon genome with living Asian and African Elephants as well as with the previously published genome similarly ‘back of the freezer’ Mammoths (Mammuthus primigenius). Here’s their tree:

Rohland et al 2007 image links to original, larger version.

The also compared these genomes to elephants’ closest living relatives, Hyraxes and Dugongs (remind me to write about Afrotheria some time…), as well as compared the rate of genetic change in proboscideans with other mammals, including primates.

Snap! (Skull tip to Afarensis)

Hey, what’s that thing by Charles Peale’s foot? A meat grinder? To be continued?