The roots of the mammalian family tree have long been shrouded in mystery — when did the placental mammals go their separate ways? Now, researchers at the University of Bristol say they’ve found where the family tree of placental mammals first branched apart — and when it happened. Their findings were first published online on 5 January in the journal Genome Biology and Evolution.
The controversy
Placental mammals consist of three main groups that diverged rapidly, evolving in wildly different directions: Afrotheria (for example, elephants and tenrecs), Xenarthra (such as armadillos and sloths) and Boreoeutheria (all other placental mammals). 
The relationships between them have been a subject of fierce controversy with multiple studies coming to incompatible conclusions over the last decade leading some researchers to suggest that these relationships might be impossible to resolve.
There are thus many outstanding questions such as which is the oldest sibling of the three? Did the mammals go their separate ways due to South America and Africa breaking apart? And if not, when did placentals split up?
“Now we’ve proven these problems can be solved — you just need to analyse genome-scale datasets using models that accurately reflect genomic evolution,” added Tarver.
The study
The researchers assembled the largest mammalian phylogenomic dataset ever collected before testing it with a variety of models of molecular evolution, choosing the most robust model and then analysing the data using several supercomputer clusters at the University of Bristol and the University of Texas Advanced Computing Centre.
“We tested it to destruction,” said Dr Tarver. “We threw the kitchen sink at it.”
“A complication in reconstructing evolutionary histories from genomic data is that different parts of genomes can and often do give conflicting accounts of the history,” said Dr Siavash Mirarab at the University of California San Diego, USA. “Individual genes within the same species can have different histories. This is one reason why the controversy has stood so long — many thought the relationships couldn’t be resolved.”
To address the complexities of analysing large numbers of genes shared among many species, the researchers paired two fundamentally different approaches — concatenated and coalescent-based analyses — to confirm the findings.
The findings
When the dust settled, the team had a specific family tree showing that Atlantogenata (containing the sibling groups of African Afrotheria and the South American Xenarthra) is the sister group to all other placentals.
Because many conflicting family trees have already been published, the team then gathered three of the most influential rivals and tested them against each other with the same model. All of the previous studies suddenly fell into line, their data agreeing with Tarver and colleagues.
Results from four of the phylogenetic analyses with each one providing support for Atlantogenata as the sister taxon to all other eutherians. (a) The 21.4 million whole-genome nucleotide alignment analyzed using Phylobayes (CAT-GTR+G), RAxML and ASTRAL with support values for almost all nodes being either 1 or 100. (b) The single concatenated nucleotide alignment for the pre-mir sequences analyzed under GTR+G in Phylobayes. Laurasiatheria is shown collapsed as the interrelationships among the constituent taxa vary between data sets.
James E Tarver, et al. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. (2016) 8 (2): 330 – 344. doi: 10.1093/gbe/evv261; Creative Commons Attribution License
With the origins of the family tree resolved, what does this mean for placental mammals? The researchers folded in another layer — a molecular clock analysis. “The molecular clock analysis uses a combination of fossils and genomic data to estimate when these lineages diverged from each other,” said author Dr Mario Dos-Reis of Queen Mary London, UK. “The results show that the afrotherians and xenarthrens diverged from one another around 90 million years ago.”
The conclusions
Previously, scientists thought that when Africa and South America separated from each other over 100 million years ago, they broke up the family of placental mammals, who went their separate evolutionary ways divided by geography. But the researchers found that placental mammals didn’t split up until after Africa and South America had already separated.
Results from the molecular clock analysis showing the divergence times for placental lineages with all posterior probabilities shown in “green” and overlaid on the joint prior shown in “red,” with both shaded to show values of highest likelihood (see table 6 for the 95% HPD values). Current biogeographic reconstructions for the breakup of Pangea at 180, 120, and 90 Ma, from “left to right,” respectively, with hotter colors (“red”) indicating faster rates of sea floor formation than colder colors (“blue”) based on Seton et al. (2012) and downloadable from http://www.earthbyte.org/Resources/global_plate_model_ESR12.html. Both the Northern and Southern hemisphere continents have separated by 90 Ma, highlighting the role of dispersal, rather than vicariance, for the biogeographic distribution of crown placentals as the breakup of Pangaea predates current molecular clock estimates for the divergence of crown placentals.
James E Tarver, et al. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. (2016) 8 (2): 330 – 344. doi: 10.1093/gbe/evv261; Creative Commons Attribution License
“We propose that South America’s living endemic Xenarthra (for example, sloths, anteaters, and armadillos) colonized the island-continent via overwater dispersal,” said study author Dr Rob Asher of the University of Cambridge, UK.
Dr Asher suggests that this isn’t as difficult as you might think. Mammals are among the great adventurers of the animal kingdom, and at the time the proto-Atlantic was only a few hundred miles wide. We already know that New World monkeys crossed the Atlantic later, when it was much bigger, probably on rafts formed from storm debris. And, of course, mammals repeatedly colonised remote islands like Madagascar.
Even sloths can swim 
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“You don’t always need to overturn the status quo to make a big impact,” said Dr Tarver. “All of the competing hypotheses had some evidence to support them — that’s precisely why it was the source of such controversy. Proving the roots of the placental family tree with hard empirical evidence is a massive accomplishment.”
(Source: University of Bristol press release, 15.02.2016)
