This is a good example of the kind of pseudoscience I'm after. The claim is that at some point, seemingly in the second millennium BCE, there was a vast "Kushite" empire extending from what is now Ghana and Morocco to India and the Caspian Sea, traceable through allusions in the Classical literature and genetics. There is no support for such an empire, which would be completely unprecedented in world history, and, while I haven't done the calculation, would probably be the largest land empire in the history of the planet. The evidence in favour of it is very poor. The author is deeply confused about language families, the history of the Near East, and many other topics about which she pontificates, and she is putting out information that is flat out wrong. I'm going to try to untangle some of these issues, but not all of them - I want to write a blogpost, not clean out the Augean stables.
The first piece of evidence alluded to is genetic. The R-M173 haplogroup is used alongside linguistic data to claim that an empire once existed that stretched over the area covered by the haplogroup. A map of the haplogroup is to be found on the site, and is used not as a map of the genetics alone, but of the empire itself. If you look at the map, you'll see that it corresponds quite well with the areas in which Islam is to be found in the majority today (except for the Malay archipelago and Turkey). It corresponds with the areas that were under the control of Arab warlords after the rise of Islam in the seventh century or which have had sustained contact with Arab, or at least Afroasiatic-speaking civilizations, for a sustained period - which works much better with the data and which came, you will note, somewhat later than the second millennium BCE.
Excluding west Africa and Greater Persia, it is also a fairly accurate map of the spread of the Afroasiatic languages - but it is vital to note that speaking a related language doesn't mean being part of the same political entity (to believe this you'd have to assume that almost all of Europe, North America, South America, north India, Pakistan, Iran, and parts of Africa are parts of one great political confederation today). Oh, and the links between archaeological culture, existing populations, genes, and languages are difficult to make perfect sense; you certainly can't assume that people sharing a language also share genes (although there does seem to be considerable overlap in most instances).
Unfortunately, the map - courtesy of a very dodgy paper to be found here - provides no data on concentrations of the haplogroup, showing only a blanket across Afro-Eurasia, and so nothing can be told from the map regarding its origins. I'm not a geneticist, and I don't have the expertise to create a map from the data given in the paper. The paper may be fine on the genetics for all I know; what matters are the claims based on other sources, because those are the wellspring for the claim that the genetic evidence equals an ancient empire. The paper cites Herodotus and a cryptic passage from Homer to claim that the genetics correspond to a Kushite civilization. Herodotus indeed claimed that the Kushites ruled Babylon in ancient times, and he claimed to have received his information from Egyptians (IIRC, it is in Book II that he makes these claims). But he didn't speak Egyptian, nor Meroitic, nor Persian for that matter, and as Egypt had been invaded by the real Kushites in the 8th century BCE, it is entirely possible that he was confused. As indeed he was.
Anyway, back to the blogpost. The author of the post, Alice Linsley, claims that the Hapiru or Habiru were Kushite priests and religious officiants. The word Habiru is actually a very interesting word; it crops up a fair number of times in Egyptian and Near Eastern writings from the second millennium BCE (meaning that it fits the timescale of the pseudoscience claims), but it means in every instance a kind of vagabond community derived from the kingdoms overrun either by the Hittites, Egyptians, or, later, the Assyrians. Canaan, the Syrian cities, Aramaean communities - all of them seem to have contributed to the Habiru, and the consensus (at least, the consensus represented in Marc van de Mieroop's fairly recent A History of the Ancient Near East) is that the Habiru (one possible source of the word Hebrew) were a group of nomadic pests bothering the settled civilizations, who drew away their disgruntled members. Such communities are perhaps exemplified by those studied in the work of the anthropologist James C. Scott, who looked at the history of southeast Asia through the effects of communities like this in a wonderful book called The Art of not Being Governed. Linsley disingenuously uses quotes from reputable sources, including an article by Carol Redmount on the history of Israel in Egypt, in an attempt to legitimise the fringe claim that the Habiru were African Kushite priests, when this is in fact nonsense with no reasonable evidence behind it.
Far from being priests of an ancient and powerful empire stretching across two continents, the Habiru were semi-nomadic groups recruiting disaffected people from settled communities. Not only does this accord with the data we have, it makes much more sense in a time before telecommunications than a vast intercontinental empire (which, suspiciously, seems to have generated no written texts). Running an empire requires a bureaucracy. It requires lots of willing supporters and military force, but it requires more than anything an ability to hold the domain together through establishing contacts between everyone in it, and this is why Herodotus stresses the role of Persian couriers in maintaining the then-largest empire in history. This is a very difficult and costly thing to do, and there's no evidence of this being in place, connecting Ghana and Pakistan, in the second millennium BCE.
Before continuing, I'd like to pick up this point. Genetic studies point to similarities between people in Nigeria and people in Iran, according to that paper. Let's assume it's true. Why is it that people in Iran, north Africa, the Mediterranean, Europe, India, Arabia, Mesopotamia, and Anatolia all developed scripts based on one of two precedents (Egyptian or Sumerian), but people in west Africa - supposedly deeply connected to Egypt, the ultimate source of our current script - did not? This has always been one of the biggest of the many gaping holes in Afrocentric theories. If a Kushite empire had stretched across this land and was held together in the same way every empire in history has been (through a large bureaucracy [written or unwritten], extensive internal trade, and the power of a loyal, flexible army), why did the Egyptian invention of writing, developed much earlier than the second millennium BCE, not penetrate into sub-Saharan Africa until its introduction by Arabs and Europeans?
Habiru is not the only spurious term in the post; many more follow, from the supposedly Egyptian derivation of Angkor Wat (which was, of course, built around the 8th century CE, about three thousand years after the heyday of this entirely fictional dominion and outside the limits provided by the map) to claims that Sanskrit, Arabic, and the Dravidian languages are all related. The reality behind these claims is much more interesting and complicated than the claim that they are related to each other, but I don't have time to outline it all. Suffice it to say that Angkor was built by Khmers (and comes from their pronunciation of the Sanskrit word nagara, meaning 'nation' or 'city', amongst other things); Sanskrit is an Indo-European language unrelated to Tamil, Malayalam, Brahui, and the other Dravidian languages of India; and Arabic is a Semitic language related to Hebrew, Akkadian, and Ugaritic, and more distantly related to Egyptian and Ge'ez.
The evidence provided in the post amounts to a list of false cognates. A false cognate is any word that has a similarity to a word of similar meaning in another language, but is not demonstrably related to it. For instance, the word for "dog" in Mbabaram, an Australian language of the Pama-Nyungan family, is dog. English and Mbabaram are not related, and the word dog in both languages has a known derivation. That's a false cognate. The entire list provided by Linsley consists of known false cognates.
Another of Linsley's claims is this: "The conquest of the Sumerian city states by Kushites rulers is well-documented." In fact, this is nonsense. Linsley turns Kish, a Sumerian city-state in northern Babylonia, into Kush, an African empire that overran Egypt a couple of thousand years after Kish's rise. They are not at all related. Her claim that Herodotus says that the Kushites overran Babylon is backed up by The Histories - but Herodotus certainly got it wrong. A group of invaders, possibly speaking a Hurro-Urartian language or a language isolate (ie, not a Nilo-Saharan nor Afroasiatic language) did invade and assume control of Babylonia for several centuries in the second millennium BCE, but they're called the Kassites, not the Kushites, and they weren't Africans. Herodotus got it wrong. How do we know? The Kassites produced written sources of their own, they recorded a few bits and pieces in their own language, and they are mentioned by other sources in the region, especially those in Babylonian, the language of the region they conquered (and which they themselves used for most things), as well as those from Egypt. They weren't unknown people from Africa who created a vast empire, or anything even remotely close to that.
Another flaw appears in the genetics article provided as evidence by Linsley. A very common mistake is provided as if it were not a mistake at all: the article claims that the Kushans, Indo-European-speaking central Asian-derived nominal Buddhists who ruled parts of India in the first century CE (again, over a thousand years after the end of second millennium BCE), were Kushites. This is not borne out by any evidence, and is simply an outright mistake predicated entirely on the fact that "Kush" and "Kushan" are fairly similar in sound. The link provided by the author of the paper got his claim from Armenian sources (calling the Kushans "Qushani"), neglecting the fact that the Armenians (Indo-European speakers) are recent arrivals in the Caspian region, who would have had no experience of an Afroasiatic empire in the second millennium BCE because they didn't live in Armenia then (at that time, the place we now call Armenia was home to Hurro-Urartian speakers).
Importantly, we're talking about quite a well-documented period of history. We have collections of texts from Egypt, Assyria, the Hittite empire, Mycenaean Greece, and Babylonia from a variety of archaeological sites that discuss and provide detailed evidence of politics, gift-giving, and cultural exchange in the second millennium BCE. Working out the international scene in the eastern Mediterranean, Egypt, and Mesopotamia in that period is relatively straightforward (except in the Hittite empire, where the names of rulers are fairly ambiguous). There is no evidence in, say, the incredible Amarna letters, letters from Akhenaten's personal diplomatic correspondence stash, that there was a vast African Kushite empire at this time - or any time, for that matter.
The "Afroasiatic Dominion" idea is demeaning to the real Kushites, Nubians, and Meroitics, who really did rule a very real African empire, who really were "black" (as if that is a meaningful biological term anyway), who really did speak a Nilo-Saharan language (probably), and who really conquered Egypt in a very real and well-documented series of invasions. They flourished together, such that during the New Kingdom of Egypt there was little meaningful distinction between Egypt and Nubia. But that is simply not the same as an inter-continental empire.
There are lots of other spurious claims. It would take a long time to go through them all. What's surprising about this is that there is a semi-coherent theory underlying the claim of "Kushite" expansion as shown in Linsley's post, in seeking a root for it in marriage patterns (which can influence the spread of populations; it's a plausible motivation for some of the spread of Austronesian-speakers across the Pacific). The problem is simply that this explanation is produced for bullshit evidence. There's nothing for the explanation to explain.
It's probably true that the pre-Indo-Aryan population of India was "Negroid", as is claimed in the post, and this is also true of the pre-Austronesian population of the Philippines and Malay archipelago, but the migration was not as recent as the second millennium BCE, and neither Dravidian-speaking Indians nor Melanesians have ancestors from an ancient African empire. In fact, the second millennium BCE is a much more reasonable estimate for the time when these native populations were overrun by invaders speaking other, unrelated, languages. There is no evidence that these communities were all linked by a single overarching empire.
And this is the fundamental, underlying assumption behind the idea that there was a such an empire: the idea that genetics and linguistics prove a political relationship. But genetics simply doesn't equal politics. The fact that a group of people shows a genetic relationship to another does not mean that all of those people got along, or formed a small nation, let alone a large empire. All it shows is that they share a common ancestor or set of ancestors whose genes they carry (and this is assuming that the genetic evidence is reliable; bear in mind that we only have access to populations in these places today, with only a few older samples, and globalisation has had impacts everywhere). This, I think, is the moral: do not make radical claims on the basis of incomplete and spurious evidence, especially when all of the other extant evidence contradicts the claim. It is important to value the truth more than baseless but appealing speculation.