Most methods of phylogenetic analysis deal with simple trees. In these phylogenies, every taxonomic unit has a single direct ancestor (or “parent”). But we know that phylogeny is often more complex than this. Our own species is an excellent example—while we are all primarily descended from one population in Africa, different peoples around the globe have inherited smaller percentages of ancestry from preexisting populations.
Operational Taxonomic Units
Reich & al. used the following nine populations, seven extant and two extinct, as operational taxonomic units.
|Yoruba.—An ethnicity from West Africa (Nigeria, Benin, Ghana, etc.)
(Photo by Marc Trip.)
|Han.—The most populous Chinese ethnicity.
(Photo by Brian Yap.)
|Mamanwa.—One of the “Lumad” (“indigenous”) ethnicities of the southern Philippines.
(Photo by Richard Parker.)
|Jehai.—One of the Orang Asli (“original people”) groups of Malaysia.
Note: this photo is of a woman from a different Orang Asli tribe, the Batik.
(Photo by Wazari Wazir.)
|Onge.—A group of Andaman Islanders, from the Bay of Bengal.
(Photo from The Andamanese, by George Weber.)
|Australians.—The indigenous (“aboriginal”) peoples of Australia.
(Photo by Rusty Stewart.)
|Papuans.—The indigenous peoples of the New Guinean highlands.
(Photo owned by the Center for International Forestry Research.)
|Neandertals.—An extinct group of robust near-human peoples from West Eurasia.
(Photo by myself, of a sculpture by John Gurche.)
Reich & al. postulated the simplest phylogeny that could possibly explain their data. (Note that the actuality is likely more complex than this, but it’s a good starting point.) More recent groups are to the right, and the thickness of the lines indicates the percentage of DNA contributed from population to population.
|My diagram, not theirs. Any inaccuracies are my own.
Free for reuse under Public Domain.
I’ve added a line for the Denisovans’ mitochondrial (motherline) ancestor, even though it’s not part of the paper’s phylogeny. More on that as we start looking through the various clades.
For looking at the clades I’ll use a different diagram that does not reflect percentage of ancestry, but simply shows direct descent as unweighted arcs connecting parent and child taxonomic units.
|Phylogeny of human and near-human populations according to Reich & al. 2011.
Created using Names on Nodes.
Free for reuse under Public Domain.
Mitochondrial DNA Crown Group.—Although most Denisovan DNA shows shared ancestry with Neandertals, exclusive of humans, the mitochondrial DNA tells a different story. Denisovan mtDNA diverged from human-Neandertal mtDNA a very long time ago, perhaps around a million years ago.So we begin with this, the oldest clade of the human total group wherein mtDNA is known for all direct sub-branches.
From the timing, the ancestor of this clade might be Homo antecessor or a similar contemporary. There are two main branches that we know of: one which produced Neandertals, humans, and the nuclear component of Densiovan ancestry, and the other of which produced the mitochondrial component of Denisovan ancestry. Perhaps as Denisovans migrated eastward over Asia they mated with the females of another lineage.
Nuclear DNA Crown Group.—This is the oldest clade represented by nuclear DNA, roughly 400 millennia old. The ancestors of this clade would probably be classified as Homo heidelbergensis. Two major subclades are known: one leading to humans and the other to “archaic” Eurasians (Neandertals and Denisovans).
Strictly speaking, there is an even older nuclear ancestor, since another study indicates that some South and Central Africans inherited some nuclear DNA from an ancestor that split off around 700 millennia ago. But those populations aren’t covered by this phylogenetic hypothesis.
Humans.—Humans (in the strict sense) are a crown group that originated in Africa roughly around 200 millennia ago. Some, such as the Yoruba, are descendants of those who stayed in Africa. Those who left Africa, into Eurasia, mixed with the “archaics” already living there.
|“Neanderthaloids”.—This clade includes Neandertals and their (partial) descendants, the Eurasian humans. (There’s no existing name for it so I just made one up.)|
|Eurasian Humans.—Eurasian humans are mostly descended from early African humans, but have inherited 1–4% of their DNA from Neandertals.|
|“Denisovoids”.—This clade includes Denisovans and their (partial) descendants, the indigenous peoples of Oceania. (As with “Neanderthaloids”, there’s no existing name for the clade so I just made one up.)|
Mongoloids.—These peoples originated in East Asia. Reich & al. find two major subclades. One includes the Orang Asli peoples of Malaysia (such as the Jehai and Batik), who are also part Australoid. The other leads to Chinese and Filipino peoples.
|“Sinoids”.—Traditionally “Sinoid” is a synonym of “Mongoloid”, but here I am using it for the subclade of Mongoloids including Chinese and Filipinos. Indigenous Filipinos (Lumad peoples, such as the Mamanwa) are also part “Denisovoid” Oceanian.|
Clades with Multi-Unit Cladogens.—This is a clade. One of its possible definitions is branch-based: the clade stemming from the initial ancestor of Australians and Han Chinese which was not also ancestral to [late Siberian] Denisovans. But if you look closely, there’s something odd about this clade (my apologies that it’s not a bit easier to see). Namely, the “ancestor” of this clade is two taxonomic units! One is the “Neanderthaloid” ancestor and the other is the human ancestor.
But isn’t a clade supposed to be “an ancestor and all of its descendants”? Well, as I discussed in my 2007 paper and more recently on Names on Nodes, we need to define exactly what we mean by “ancestor”. I define a clade ancestor, or cladogen, as a union of one or more taxonomic units wherein 1) none of the units are ancestral to each other, and 2) there exists at least one other unit which is descended from (or equal to, in case the cladogen is a single unit) all of the units in the cladogen. The union of the ancestral populations of “Neanderthaloids” and humans, respectively, satisfies these conditions. They can be seen as part of a population that does not include the Denisovans, since they share descendants that do not have Denisovan ancestry (including, e.g., the Han, West Negritos, … and myself!) So, even though they consist of two units in this study, they still comprise a population and can be used as a clade ancestor.
Studies like this one may seem to some to test the usefulness of phylogenetic nomenclature, since it features clades that overlap. In fact, phylogenetic nomenclature has always allowed for overlapping clades. It is phylogenetic analyses that routinely assume no overlap. In many cases this is useful, but I tend to wonder if it doesn’t obscure our vision in a lot of cases. Studies like this one are encouraging to me, since they move toward embracing the fact that Life is not a simple tree.