Rewriting Elephant History
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The story as of a few years ago is that there were two living species of elephant, the African and the Asian. The former was classified in the genus Loxodonta, and the later in Elephas. The one surviving member of Elephas is the Asian elephant Elephas maximus. 6 or 7 million years ago, a paleoelephant from Africa migrated out of Africa and became the progenitor of today's Asian elephant.
In recent years, the weight (pardon the pun!) of the evidence is that there are two distinct African species, the savannah or bush elephant, and the smaller forest elephant largely confined to the Congo region. These are called respectively Loxodonta africana and Loxodonta cyclotis. Thus there are three living species of elephant.
So how to classify the extinct paleoelephants of which we have some, though limited, fossil evidence? There are a number of species of extinct Eurasian and African straight-tusked elephants classified under the genus Palaeoloxodon. As far as I can tell, the oldest of these date from 4 million years ago to others still extant maybe 20 or 30 thousand years ago. Morphological, they resemble Asian elephants, so that some scholars have wanted to place them in the genus Elephas. In that schema, the broad Asian phylogeny (often seen as including Mammoths) spread across Eurasia and North America.
What is new? DNA evidence is now able to shed some light on these relationships. It turns out that the morphological similarities lead to erroneous conclusions. The Palaeoloxodon elephants are genetically on the same branch as Loxodonta, not Elephas. And here's the shocker: they fall not directly onto the L. africana line, but rather the forest elephant line, L. cyclotis.
So the situation now, where the forest elephant looks like a rump population, an island group, with L. africana more numerous and with a much more expansive geographic range, does not represent the situation historically. The African forest elephant once roamed more widely and is associated with species of extinct elephants widely dispersed around Africa and Eurasia.
Here's the original article:
"Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution"
oh wait, I think I remember - maybe it's from Evolution in Action which I'm in the middle of reading. hm. Let me check.
I was able to piece together some of the mammoth information, but based on my investigation, I am left to conclude that there are major unknowns left in understanding the genetic relation of the mammoth to elephants. The following* is helpful, from the U of CA Museum of Paleontology:
"Loxodonta, Elephas and Mammuthus originated in Africa during the Pliocene (about 3–4 million years ago). Loxodonta remained in Africa while Elephas dispersed from Africa twice. The first dispersal event was in the mid-Pliocene, when Elephas moved into Asia; the extant Elephas maximus is a descendant of these emigrants. The second dispersal occurred in the late Pliocene when Elephas moved into Asia and Europe, but this dispersal resulted in extinct lineages. Mammuthus disappeared from Africa by the Pleistocene but dispersed to Europe, Asia and Africa in multiple events prior to this (see Mammoths below). While all three genera lived in Africa, they did not seem to compete with each other. In southern Africa, Loxodonta and Elephas do not occur in the same fossil assemblages; in other parts of the continent, the two genera are only rarely found together. It appears that Loxodonta only becomes abundant in eastern Africa once Elephas has disappeared from the area." (http://www.ucmp.berkeley.edu/mammal/mesaxonia/elephantidae.php)
If the above is correct, it adjusts the picture I painted above. It suggests that an earlier Elephas, not Loxodonta, left Africa and became the progenitor of the Asian elephant. It is silent on the exact cladistic or genetic relation of the mammoth to extant elephants. They are not specific about the second exodus from Africa of Elephas, but it sounds like they may be suggesting that this exodus led to the "extinct lineages" we know as Palaeoloxodon. Which from the article cited in the OP appears to be false. So there is reason for skepticism about the schema they present.
The Wikipedia entry for Mammoth displays a cladogram based on morphological characteristics that is almost certainly wrong. The cladogram still shows the incorrect placement of the Palaeoloxodon genus in close proximity to Elephas:
Other sources indicate that the mammoth-elephant split occurred before the split between Elephas and Loxodonta: "'Our data suggest that mammoths and modern-day elephants separated around six-million years ago, about the same time that humans and chimpanzees separated,' said Miller. 'However, unlike humans and chimpanzees, which relatively rapidly evolved into two distinct species, mammoths and elephants evolved at a more gradual pace,' added Schuster, who believes that the data will help to shed light on the rate at which mammalian genomes, in general, can evolve."
(Webb Miller, professor of biology and of computer science and engineering and Stephan C. Schuster, Penn State professor of biochemistry and molecular biology and the project's other leader, Penn State's Center for Comparative Genomics and Bioinformatics and their Mammoth Genome Project.)
As I look at this I am struck by a few things. First, the UC Museum argues, based on morphological comparison, for a split between Elephas and Mammuthus occurring after the Elephas-Loxodonta split. (See their cladogram in the cited article) The Penn State Mammoth Genome Project researchers clearly argue for an early Mammuthus split. Such discrepancies are common in the process of trying to establish evolutionary relationships among over species as well. Neither has yet publicly addressed the recent article I cite in the OP redrawing the phylogenetics of the genus Palaeoloxodon and its relation to L. cyclotis. Perhaps these matters are nearer to becoming clarified, but we're not there yet, as best I understand the state of things.
*please note that in this follow-up, I have not italicized genus and species names. I wrote this on an iPad, and including the correct html formatting to do so would have taken a prohibitive amount of time.