The Testimony Of The Goat

An new paper examining ancient goat Y-DNA and also Y-DNA from modern goats from sixteen different breeds and seven species of wild goats, largely reinforces the paradigmatic narrative regarding the expansion of farming from the Fertile Crescent Neolithic revolution already supported by archaeological and human DNA evidence. 

It turns out that all domesticated goats in the world are predominantly derived from the bezoar goat (a.k.a. bezoar ibex a.k.a. mountain goat) which is native to the vicinity of the forested parts of the highlands of Anatolia (a.k.a. Asia Minor, now mostly in a country called Turkey) and Persia (now called Iran) (more generally "West Asia") where they were one of the first animals domesticated in the Fertile Crescent Neolithic Revolution. As Wikipedia explains:

The bezoar ibex (Capra aegagrus aegagrus), also known as the Anatolian bezoar ibex, Persian ibex, or (by Anatolian locals) dağ keçisi (Turkish: 'mountain goat'), is a wild goat subspecies that is native to montane forests from Turkey to Iran.

The bezoar ibex is found in the mountains of Asia Minor and across the Middle East. It is also found on some Aegean islands and in Crete, where it is accepted that the goats constitute relict populations of very early domestic animals that were taken to the Mediterranean islands during the prehistoric period and now live as feral populations. The bezoar ibex, if not the sole progenitor of the modern domestic goat, is at least its main progenitor. The archaeological evidence traces goat domestication as far back as c. 10,500 years Before Present, and DNA evidence suggests 10,000 years BP.

In particular, the geographic distribution of goat Y-DNA shows the distinction between the LBK and Cardial Pottery waves first farmer migrations. It also shows a separate wave of goat herding migration with a different mix of lineages than in Europe, that were likely spread across Africa via the Egyptian Neolithic.

A more notable finding is that almost all domesticated South Asian, Southeast and East Asian goats, other than those arriving within the  modern era (i.e. starting no earlier than last five hundred years or so, and perhaps even in the 20th century) in Korea and Japan, appear to be derived from lineages (some of which are rare in Europe and Africa) of Fertile Crescent Neolithic Iranian goats, rather than deriving from an independent domestication. This indicates that economically significant long distance trade between West Eurasia and East Eurasia at some point in the prehistoric Holocene era. The exact timing can probably be accurately estimated based upon the time at which remains of goats are first attested in these places, but that data isn't available in this particular paper.

Another interesting point is that while Madagascar was settled by a population of mixed East African and Indonesian origins, its goats all have African origins, even though its language is almost entirely Indonesian (and Austronesian) in origins. This adds another data point to the unclear question of what the nature of the relationship between the Indonesian and East African founders of Madagascar had with each other.

It is also rather remarkable how long an imprint of Neolithic migrations seem to have endured pretty much worldwide, despite significant global trade that goes deep into prehistory. The immense turnover of human populations in the Bronze Age in Europe and Southeast Asia, and in the Bantu expansion in Africa, appear to have overlooked goats.

The new preprint about this topic and its abstract are as follows:

The male-specific part of the Y-chromosome is in mammalian and many other species the longest haplotype that is inherited without recombination. By its paternal transmission it has a small effective population size in species with dominant males. In several species, Y-chromosomal haplotypes are sensitive markers of population history and introgression. Previous studies have identified in domestic goats four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional variants. In this study we used published whole-genome sequences of 70 male goats from 16 modern breeds, 11 ancient-DNA samples and 29 samples from seven wild goat species.  

We identified single-copy male-specific SNPs in four scaffolds, containing SRY, ZFY, DBY with SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated haplogroups corresponding to the haplotypes Y1B, Y2A and Y2B, respectively, but Y1A was split into Y1AA and Y1AB. All haplogroups were detected in ancient DNA samples from southeast Europe and, with the exception of Y1AB, in the bezoar goat, which is the wild ancestor of the domestic goats. Combining these data with those of previous studies and with genotypes obtained by Sanger sequencing or the KASP assay yielded haplogroup distributions for 132 domestic breeds or populations. The phylogeographic differentiation indicated paternal population bottlenecks on all three continents. This possibly occurred during the Neolithic introductions of domestic goats to those continents with a particularly strong influence in Europe along the Danubian route. This study illustrates the power of the Y-chromosomal haplotype for the reconstructing the history of mammalian species with a wide geographic range.

Isaäc J. Nijman, et al., "Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats" bioRxiv (February 17, 2020) doi: https://doi.org/10.1101/2020.02.17.952051

From the body text (citations omitted):

A preliminary analysis of the Y-chromosomal diversity in European and Turkish goats defined the three haplotypes Y1A, Y1B and Y2, showing strong geographic differentiation. The same haplotypes were found in goats from Portugal and North-Africa, Turkey, east and south Asia, Switzerland and Spain with additional haplotypes Y2B in east Asia, Y2C in Turkish Kilis goats, and Y1B2 as well Y1C mainly in Switzerland. . . . 

Remarkably, with the exception of Y1B the haplogroups have all been found in Iranian bezoar samples, whereas all haplogroups, including Y1B, were detected in ancient goat samples. 

Geographic plots of haplogroup frequencies show a considerable spatial differentiation, which resonates the strong phylogeography displayed by autosomal SNPs, but is in clear contrast with the phylogenetic structure displayed by mtDNA haplogroups. Most likely, by a series of bottlenecks in the male lineage subcontinents have different major haplogroups, while none has a global-wide coverage:

- Haplogroup Y2B is absent in Europe, Africa and west Asia, but became a major haplotype in east Asia and southeast Asian, where Y2A is not represented. In contrast, it is observed in ancient goat from Medieval Georgia and Neolithic Iran (ca. 6,000 BCE), supporting an origin of east Asian goat from regions east of Zagros Mountains.

- Y2A is in northern and central Europe only found in the crossbred AngloNubia, but is the predominant haplogroup in central, eastern and southern Africa.

- Haplogroup Y1B is predominant in northern Europe, but outside Europe and North African has only been found in one Karamonja animal, in the Korean native breed and in exported Saanen populations. 

The different Y2A and Y1B frequencies in north-central vs southern Europe may reflect the Neolithic migrations following the Danube and the Mediterranean routes, respectively with the strongest bottlenecks along the northernmost migrations.

- Y1AA is sporadic in Europe and has been observed also in Neolithic Serbia (ca. 6,000 BCE), but is present in Asia. 

Deviations from the general pattern may very well reflect major introgressions. A well-known example is the Anglo-Nubian, which originated in England by crossing Indian or African imported goats with local breeds and is in our panel the only northern-European breed carrying Y2A. 

There were two out-of-range findings of Y1B, in the Uganda Karamonja and in the Korean native breeds. Because of the popularity of Swiss dairy goats in both Uganda and Korea, crossbreeding again is the most likely explanation. 

Fig. 2.

Haplogroup distributions of (A) European breeds; (B) Asian breeds; (C) African breeds; (A, B), European and Asian ancient DNA samples; and (B) Iranian bezoars. 

Breeds represented by a single goat are not plotted or are combined with other breeds from the same country. 

Breed codes: ABA, Abaza; ALP, Alpine; ANB, AngloNubian; AND, Androy; ANK, Angora;Ankara; APP, Appenzell; ARA, Arabia; ARG, Argentata dell’Etna; ARR, Arran; ARW, Arapawa; BAG, Bagot; BAL, Balearic; BBG, Black Bengal; BEY, Bermeya; BHU, Bhutan; BIO, Bionda dell’Amadello; BLA, Blanca Andaluzza; BLB, Bilbery; BLO, Blobe; BOE, Boer; BRA, British Alpine; BRV, Bravia; BUK, Polish Fawn Colored; CAM, Cambodja; CAP, Capore; CHN, North China (Xinjiang, Henan Raoshan White, Shandong); CHQ, Charnequeira; CHV, Cheviot; COR, Corsican; CRO, Croatian Spotted; CRP, Carpathian; DIA, Diana; DJA, Djallonke; DKL, Danish Landrace; DPG, Dutch Pied Goat; DRZ, Dreznica; DUK, Dukati; DUL, Dutch Nordic Goat; ESF, Esfahan; ETH, Ethiopian (Abergelle, Gumez, Keffa); FIN, Finnish; FLR, Florida; FUE, Fuenteventura (Ajuy, Majorera); GAL, Galla; GAR, Garganica; GDR, Guadarrama; GGT, Girgentata; GMO, Grigia Molisana; GRG, Greek; GRS, Grisons Striped; GUE, Guéra; GUR, Gurcu; HAI, Hair; HAS, Hasi; HNM, Honamli; IND, Indian; IRA, Iranian; JPA, Shjiba; JSA, Japanese Saanen; KIG, Kigezi; KIL, Kil; KLS, Kilis; KMO, Karamonja; KON, Korean Native; KSA, Korean Saanen; LAO, Laos; LBA, Lori-Bakhtiari; lCL, Icelandic; LIQ, Liqenasi; MAK, Makatia; MAT, Mati; MAU, Maure; MEN, Menabe; MGL, Mongolian; MLG, Malagueña; MLI, Naine, Soudanaise Targui; MLT, Maltese; MLW, Malawi (Balaka-Ulonge, Dedza;Lilongwe; MOR, Moroccan; MSH, Mashona; MTB, Matebele; MUB, Mubende; MUG, Murciano Granadina; MUL, Mulranny; MUZ, Muzhake; MYA, Myanmar; MZA, M’Zabite; NCG, Norwegian Coastal; NDG, Norwegian Dairy; NDZ, Norduz; NGD, Nganda; NKA, Naine de Kabylie; ORO, Orobica; PCG, Peacock; PEU, Peulh; PHI, Philippines; PIZ, Pinzgauer; PYR, Pyrenean; PYY, Payoya; QHI, Qinhai; RAS, Rasquera; ROV, Rove; RSK, Nigerian Maradi (Red Sokoto); SAA, Saanen; SAR, Sarda; SCA, Shaanbe Cashmere; SDN, Sudan; SEA, Small East African (Kenya, Uganda); SEB, Sebei; SRP, Serpentina; SER, Serrana; SGB, St Gallen Booted; SHL, Shahel; SHL, Nigerian Sahel; SKO, Skopelos; SOF, Sofia; SOU, Southwest; SSG, Steirische Schecken; TAS, Tauernschecken; TER, Teramo; TIB, Tibetan; TNF, Tinerfena (Norte, Sud); TOG, Toggenburg; TWZ, Thuringian Forest; VAL, Valdostana; VBN, Valais Blackneck; VIE, Vietnam; VRT, Verata; VZC, Verzasca; WAD, West African Dwarf; ZAR, Zaraiba.

Missing Links On The Journey From Borneo To Madagascar

A linguistically Austronesian population from Borneo Indonesia (with strong genetic ties to Eastern Indonesia as well) settled Madagascar sometime in the vicinity of 2000 to 1000 years ago, split roughly 40% Indonesian-60% East African, with the African language vanishing on Madagascar.

Until now, however, there have been precious few bits of evidence for where they went along the way on this epic journey (there is some indication that some Southeast Indian women were added to the group en route). 

A new paper, using very solid method that fully leverages what we know already, however, changes all of that by finding residual traces of Austronesian genetics in South Arabia and East Africa, both of which are natural stopping points en route to Madagascar. The paper takes the rare step of making high quality use of interdisciplinary research from linguistics, archaeology, anthropology and history to supplement and inform its genetic analysis.

The Austronesian dispersal across the Indonesian Ocean to Madagascar and the Comoros has been well documented, but in an unexplained anomaly, few to no traces have been found of the Austronesian expansion in East Africa or the Arabian Peninsula. To revisit this peculiarity, we surveyed the Western Indian Ocean rim populations to identify potential Austronesian genetic ancestry. We generated full mtDNA genomes and genome-wide genotyping data for these individuals and compared them with the Banjar, the Indonesian source population of the westward Austronesian dispersal. 

We find strong support for Asian genetic contributions to maternal lineages and autosomal variation in modern day Somalia and Yemen. Surprisingly, this input reveals two apparently different geographic origins and timings of admixture for the Austronesian contact; one at a very early phase (likely associated with the early Austronesian dispersals), and a later movement dating to the end of nineteenth century. These Austronesian gene flows come, respectively, from Madagascar and directly from an unidentified location in Island Southeast Asia. This result reveal a far more complex dynamic of Austronesian dispersals through the Western Indian Ocean than has previously been understood, and suggests that Austronesian movements within the Indian Ocean may have been part of a lengthy process, probably continuing well into the modern era.

Nicolas Brucato, et al., "Evidence of Austronesian genetic lineages in East Africa and South Arabia: complex dispersal from Madagascar and Southeast Asia" Genome Biology and Evolution, evz028 (February 4, 2019) https://doi.org/10.1093/gbe/evz028 Full text here.

The new study suggests a presence in what is now Yemen and Somolia, ca. 1500-1800 years ago, followed by an arrival in Comoros and Madagascar ca. 800-1200 years ago. (Other sources suggest an arrival in Madagascar closer to 1500 years ago)  which ties up the dates even more tightly (or perhaps even earlier). (One is tempted to think that the same climate event the helped to cause the Roman empire to collapse may have also motivated this journey in some way, given the increasingly precise timing.)

While the authors don't jump to this conclusion, these intermediate traces of Austronesian DNA due to admixture in the right time period suggest that the Austronesian seafarers who eventually settled in Comoros and Madagascar probably followed something close to a coastal route around the Indian Ocean, rather than traveling straight across the Indian Ocean from Indonesia.

The most direct route that they could have taken which would leave the known genetic traces is illustrated with black arrows (supplied by me) on the map below (and in truth, the initial route demonstrated by the first long black arrow probably actually more closely tracked the coastline). The green arrow from Indonesia to Madagascar is now disfavored.

Of course, this something we could have guessed already based upon the fact that the modern people that the African component in Malagasy people most resemble is East African Bantus (probably close to modern Kenyan Bantus than to modern Somalis, in fact), suggesting yet another stop on the African coast before arriving in Comoros and Madagascar. Another study suggests that the African component may be closer to modern South African Bantus than to East African Bantus, but this might simply reflect the fact that modern East African Bantus have Nilo-Saharan admixture that is absent in modern South African Bantus.

We also know that it is likely that there was a stop in India because the Malagasy people have a small percentage of South Asian admixture, again, reinforcing the coastal journal model.

The study also identifies an individual whose origins appear to derive from a subsequent back migration from Comoros or Madagascar to Yemen in the 1800s, likely corresponding to historically attested trade networks associated to some degree with the ethnicity of Yemenis among whom the individual with the more recent ancestry was found.

More details from the body text are found below the fold.

Were Humans Present In Madagascar In The Early Holocene?

Austronesian together with East Africans arrived in Madagascar around 500 C.E. and dramatically changed the island's ecology, among other things, causing megafauna extinction. There is solid evidence of much more marginal human occupation that had only modest ecological impact about 2500 years before then (i.e. about 2000 BCE).

A new study argues that a couple of isolated elephant bird bones showing signs of cuts that look like they were butchered from ca. 8500 BCE, constitute evidence of a much earlier, if potentially even more marginal, early human occupation. 

But, in the absence of corroboration in the form of stone tools or human remains or other more definitive evidence of a human presence, this find merely provides a plausible reason to look for more evidence rather than truly establishing a human presence. In my view, it is too easy for a rare outlier non-human caused event to look like a butchered bone for this thin evidence pushing back the earliest potential human occupation of the island by 6500 years, for this evidence alone to establish what it is trying to prove.

Previous research suggests that people first arrived on Madagascar by ~2500 years before present (years B.P.). This hypothesis is consistent with butchery marks on extinct lemur bones from ~2400 years B.P. and perhaps with archaeological evidence of human presence from ~4000 years B.P. We report >10,500-year-old human-modified bones for the extinct elephant birds Aepyornis and Mullerornis, which show perimortem chop marks, cut marks, and depression fractures consistent with immobilization and dismemberment. Our evidence for anthropogenic perimortem modification of directly dated bones represents the earliest indication of humans in Madagascar, predating all other archaeological and genetic evidence by >6000 years and changing our understanding of the history of human colonization of Madagascar. This revision of Madagascar’s prehistory suggests prolonged human-faunal coexistence with limited biodiversity loss.

J. Hansford et al. Early Holocene human presence in Madagascar evidenced by exploitation of avian megafauna. Science Advances. (September 12, 2018). doi:10.1126/sciadv.aat6925.

We Know Precisely How People From Madagascar Ended Up As Slaves In The U.S.

In the study population genetics and prehistory, the question of how people with particular genes ended up one place from a distant destination frequently have answer that are only vague surmises because we have no historical accounts and limited archaeological data. Every once and a while some bit of data is so singular that we can do better. But, that is the exception and not the rule, and still leaves myriad details of the process fuzzy.

Once historical and business records are present, however, detailed accounts can be pieced together from business records, journals and news accounts, supplemented by the usual evidence from genetics and physical anthropology.

One of the things we know is that thousands of people from Madagascar were brought to the New World as slaves.

We know this with exquisite detail that recounts:

* the exact points of departure and points of arrival,

* the precise dates of departure and points of arrival (sometimes to the hour),

* the routes taken by the ships, 

* the name of each of the ships and who owned and insured those ships, 

* the names of the crew on those ships,

* the exact number of people and their gender and approximate age on each ship, 

* how many people died en route on each individual voyage and the cause of each death,

* the purchase prices and sale prices for the slaves, and

* the manner in which the people sold came to become slaves.

Often it is even reasonably possible to determine where these people were taken as slaves after they arrived, and with DNA evidence, it is frequently possible to detect the signature of ancestry from Madagascar which is distinctive because it contains an Indonesian component.

It isn't easy reading, but a precise understanding of how historical events have actually played out is critical to developing a more accurate intuition about the narratives that underlie less well documented gene exchange events.

This component is present in a surprisingly large share of African-Americans whose New World roots are in places where people from Madagascar were delivered as slaves. This is because all contributions to a gene pool are soon found in most members of the total population after a few generations under conditions approximating panmixia which are close enough to reality in this context to be a good model of reality, even though the Madagascar component was not a huge share of the total population of slaves imported to the New World.

One In Ten Vascular Plants In Madagascar Have Asian Origins

Figure S3 from the paper cited below.

Ancient evidence of Asian crops in Madagascar provide another piece of evidence for discerning the details of this long distance mass migration of Austronesian people to Africa.

Significance 

The prehistoric settlement of Madagascar by people from distant Southeast Asia has long captured both scholarly and public imagination, but on the ground evidence for this colonization has eluded archaeologists for decades. Our study provides the first, to our knowledge, archaeological evidence for an early Southeast Asian presence in Madagascar and reveals that this settlement extended to the Comoros. Our findings point to a complex Malagasy settlement history and open new research avenues for linguists, geneticists, and archaeologists to further study the timing and process of this population movement. They also provide insight into early processes of Indian Ocean biological exchange and in particular, Madagascar’s floral introductions, which account for one-tenth of its current vascular plant species diversity.

Abstract 

The Austronesian settlement of the remote island of Madagascar remains one of the great puzzles of Indo-Pacific prehistory. Although linguistic, ethnographic, and genetic evidence points clearly to a colonization of Madagascar by Austronesian language-speaking people from Island Southeast Asia, decades of archaeological research have failed to locate evidence for a Southeast Asian signature in the island’s early material record. Here, we present new archaeobotanical data that show that Southeast Asian settlers brought Asian crops with them when they settled in Africa. These crops provide the first, to our knowledge, reliable archaeological window into the Southeast Asian colonization of Madagascar. They additionally suggest that initial Southeast Asian settlement in Africa was not limited to Madagascar, but also extended to the Comoros. Archaeobotanical data may support a model of indirect Austronesian colonization of Madagascar from the Comoros and/or elsewhere in eastern Africa.

Alison Crowther, et al., "Ancient crops provide first archaeological signature of the westward Austronesian expansion" 113(24) PNAS 6635-6640 (2017) doi: 10.1073/pnas.1522714113

From the introductory body text:

One line of evidence that has been largely overlooked in archaeological investigations of Madagascar and, indeed, eastern Africa more broadly is ancient plants. However, it is estimated that some 10% of Madagascar’s flora was introduced from elsewhere, and plant introductions include a significant number of staple crops, spices, and arable weeds of Asian origin. Historically or currently important crops on Madagascar, like banana (Musa spp.), yam (Dioscorea alata), taro (Colocasia esculenta), and coconut (Cocos nucifera), are Southeast Asian cultivars. Asian rice (Oryza sativa), which was domesticated separately in East and South Asia but is the basis of traditional agriculture across much of Madagascar today, was also widely grown in Southeast Asia by the first millennium CE. Other Asian crops, like mung bean (Vigna radiata) and Asian cotton (Gossypium arboreum), are also cultivated on Madagascar. The fact that early crop introductions to Madagascar may have arrived with Austronesian settlers seems particularly feasible given that Austronesian expansion into the Pacific was linked to the spread of a similar suite of cultivars. 

To directly explore early cultivated plants on Madagascar and their potential to inform on its colonization history, we collected new archaeobotanical data from the island as well as contemporaneous sites on the African mainland coast (Kenya and Tanzania) and nearshore islands (Pemba, Zanzibar, and Mafia) and the Comoros. These data were collected from 18 sites in total, dating between approximately 650 and 1200 calibrated years (cal) CE. The archaeobotanical datasets derive primarily from recent excavations at 16 sites, during which systematic sampling for charred macrobotanical remains at high stratigraphic resolution was conducted. They are supplemented by existing records from one of the sites (Sima) as well as data from previous excavations at two other sites in the Comoros. The combined dataset includes 2,443 identified crop remains recovered from >7,430 L sediment across the sites and is supported by 48 accelerator MS (AMS) radiocarbon dates, 43 of which were obtained directly on crop seeds.

From the conclusion:

Although the presence of Asian crops that likely originate from Southeast Asia on early sites in Madagascar corresponds well with linguistic, genetic, and ethnographic evidence for a prehistoric migration of people from this region, the finding that these crops also dominate early assemblages on the Comoros is rather unexpected. In particular, the presence of Asian crops at sites in the Comoros earlier than at sites on Madagascar is of significant interest, and although sampling and preservation biases cannot be discounted, may reflect Austronesian colonization of the Comoros before Madagascar. As noted, however, Comorians today speak Bantu languages, and in addition, preliminary molecular genetic studies suggest that they possess only a small proportion of Southeast Asian ancestry. Nonetheless, the population of the Comoros is small and has been historically subject to significant population bottlenecks and Bantu input as a result of slave raiding and trading over many centuries. Thus, it is possible that the Comoros were settled at an early date by a Southeast Asian population that was later genetically and linguistically swamped. 

Direct colonization from Southeast Asia is common to many models of Madagascar’s Austronesian settlement, particularly those put forward by archaeologists and geneticists. However, linguistics have offered another perspective, with some linguists taking the view that the remarkable unity of Bantu loanwords and grammatical features throughout Malagasy dialects can only be explained through initial Austronesian settlement on the African mainland and/or the Comoros. Early Southeast Asian presence or influence on the Comoros has also been suggested on the basis of the apparent presence of several 10th or 11th century “Austronesian-type” furnaces on Mayotte as well as findings of shell-impressed pottery at early sites on the islands. These suggested Austronesian linkages, however, have been both limited and contentious. This study suggests that they deserve reinvestigation together with the argument that the Comoros may have served as a key base for Southeast Asian commercial activity in the western Indian Ocean, including an alternative slave-trading corridor. Independent linguistic, genetic, and archaeological studies are required to examine the role of the Comoros in early Indian Ocean population movements and commercial trade.

Madagascar's Austronesians and Africans May Not Have Arrived Together

A new study of modern Madgascar's population genetics suggests that the island was first settled by a relatively gender balanced population of Austronesians followed in fairly short order by a male dominated South African Bantu-like population perhaps a century or two later who dominated in coastal areas as the Austronesians took refuge in the highlands. Over time, they then admixed.

Marijuana and Hops Were Cultivated In 4th Century BCE Madagascar

Established dates show definite human agricultural activity [in Madagascar] during the 5th century BC, with Cannabis and Humulus (Hops) visible in palynology assemblages.

From here relying on [1] (a source which cites a 4th century BCE date rather than a 5th century BCE date).

The 4th century BCE pre-dates the usually hypothesized dates at which the first Austronesians arrived (about 500-1000 years later), although it isn't clear if the previous population was viable enough to last until then. The previous population apparently had less ecological impact on the island than the Austronesians and little genetic impact on the subsequent population which was a mix of Austronesians (ultimately originating in Borneo) and East Africans.

This is mind-blowing because the usual interpretation of the pre-Austronesian population of Madgascar is that it was made up of people who unintentionally ended up there after being cast about in a storm who regressed from a possibly agriculturalist or herder origins to a foraging lifestyle. But, cultivation of these crops, neither of which is native to Madagascar, would suggest either an intentional colonization effort by nearby Africans from the coast for which there is no other archaeological evidence of long distance maritime trade, or perhaps by Yemeni and Somalian sea farers who were the first to conduct long time maritime trade in the Indian Ocean, mostly on a circuit that linked Mesopotamia with the Indus River Valley civilization with the Ethiopian coast.

In a related development, a recent paper on archaeobotany notes that Austronesians also settled the island of Comoros (which lies between East Africa and Madagascar) and probably settled it before they settled Madagascar.

Incidentally, palynology is a discipline whose most common activity according to a Google definition (the boundaries are the subject of ongoing disciplinary turf wars), is the study of pollen grains and spores, especially as found in archaeological or geological deposits.

[1] Burney, D. A; et al., "A chronology for late prehistoric Madagascar" Journal of Human Evolution. 47. pp.25- 63 (2004).

More On Madagascar's Genetic Origins

The biggest surprises of a new paper on the genetic origins of the people of Madagascar are the roughly 2/3rds African origin demonstrated when some previous estimates had been closer to 35%-50%, and more surprisingly, that the affinity of that African component to Southern African Bantu, when previous data had rejected that hypothesis in favor of an affinity to East African Bantu populations (less some recent Nilo-Saharan admixture).

Southern African Bantu have a substrate of pre-Bantu Mozambique people which is very distinctive from any extant African population to the extent that it basically constitutes a "lost race" of Africans that coincides with linguistic substrates of Bantu languages in that region indicating that the pre-Bantu people of Mozambique spoke a click language.  There are also uniparental markers private to Mozambique that are largely absent from Madagascar.  So, there are strong reasons to be skeptical of a Southern African as opposed to East African source for the African genetic contribution to Madagascar.

The lack of a strong historical connection between Mozambique across the strait from Madagascar and that island is likewise demonstrated by a lack of archaeological support for those kinds of trade ties and a lack of Southeast Asian genetic traces in mainland Africa (anywhere).

The conclusions on the Asian genetic origins side of the analysis, on the other hand, are plausible and very consistent with previous research on the topic, although the analysis does not identify indications from previous studies that the migration was probably along the Indian Ocean's coast with stops in South Asia and East Africa, rather than directly across the Indian Ocean as a graphic in the new paper misleadingly suggests.

I'll need to look more closely at the various papers involved to see if these new results can be reconciled with the prior research, and if not, to determine the likely source of the disparity.  The two-thirds percentage is probably right, but the South African Bantu affinity seems suspect. The fact that only the Asian conclusions and not the controversial African ones end up in the abstract of the paper is also notable.

The pertinent portion of the paper addressing this point states:

The admixture profile of our dataset (2183 individuals from 61 populations genotyped for 40,272 SNPs; Supplementary figures S2 and S3, Supplementary Material online), based on ADMIXTURE analyses (Alexander, et al. 2009), shows that the Malagasy genetic diversity is best described as a mixture of 68% African genomic components and 32% Asian components, corresponding well with the results of previous studies (Capredon, et al. 2013; Pierron et al. 2014). While the African ancestry component in Malagasy appears to be broadly similar to that still present today in South African Bantu, the Asian ancestry presents a more complex pattern. . . . to more specifically identify the Asian ancestry of the Malagasy genome, we performed a Local Ancestry analysis with PCAdmix (Brisbin, et al. 2012) using two proxy parental meta-populations comprising 100 individuals with African ancestry (randomly selected from Yoruba, South African Bantu, Kenyan Luhya and Somali groups) and Asian ancestry (randomly selected from Chinese, Philippine Igorot, Bornean Ma’anyan and Malay groups). . . . To expand on this, however, we inferred the population sources of the Malagasy, their relative ratios and the dates of potential admixture events with GLOBETROTTER (Hellenthal, et al. 2014), defining each population in our dataset as a donor/surrogate group and the Malagasy as the recipient, using the haplotype ‘painting’ data obtained with Chromopainter (Lawson, et al. 2012). The best fit outcome for the Malagasy was obtained under a model of a single admixture event between two sources: the Banjar representing 37% of modern Malagasy and the South African Bantu population representing the other 63% (r2 =0.99, P<0.01; Figure 2 and Supplementary table S5, Supplementary Material online). The admixture event was dated to 675 years BP (95% CI: 625-725 years BP, Supplementary table S5, Supplementary Material online), which is similar to the dates of admixture estimated by ALDER (550-750 years BP) using Banjar population in combination with the South African Bantu (Supplementary table S6, Supplementary Material online)(Loh, et al. 2013). When each Malagasy ethnic group is analysed separately, similar parental populations, admixture proportions and dates are obtained with the noticeable older by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from estimated dates towards the east coast of Madagascar (Supplementary table S5, Supplementary Material online). Crucially, these dates of genetic admixture, in agreement with a previous study (Pierron et al. 2014), reflect the midpoint or end of noticeable admixture between groups of Asian and African ancestry in Madagascar, rather than the start of this contact. Therefore they could correspond to the end of the period of the main Austronesian presence in Madagascar that started around the first millennium CE (Dahl 1951, 1991; Dewar and Wright 1993; Adelaar 1995; Cox et al. 2012; Adelaar forthcoming). On the other hand, around 1100-700 years BP, climatic changes in the South of Africa forced Bantu populations to move to more hospitable places (Huffman 2000). This South Bantu migration has previously been suggested as an explanation for the higher density of populations observed in the South of Madagascar (Beaujard 2012a). As all of our sampled groups live in the South of Madagascar, and considering that the estimated dates of admixture are more recent on the west coast (Supplementary tables S5 and S6, Supplementary Material online), it is tempting to interpret our admixture date as marking the last significant Bantu migration to Madagascar, perhaps initiated by climatic changes in Africa.

Suffice it to say that the analysis of the African side of the genetic contribution is shallow and does not rigorously compare competing hypotheses of African contributions.

The Supplemental Materials indicate that the African samples other than South African Bantu come from International HapMap, et al. (2010) (i.e. Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58. doi: 10.1038/nature09298) and Pagani, et al. (2012) (i.e. Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool. Am J Hum Genet 91: 83-96. doi: 10.1016/j.ajhg.2012.05.015). The South African Bantu sample comes from May, et al. (2013) (Genetic diversity in black South Africans from Soweto. BMC Genomics 14: 644. doi: 10.1186/1471-2164-14-644).

Another data set of Southeastern Bantu speakers referenced in May, et al. (2013) seems to overlap with the Soweto sample and derives from Schlebusch, et al., "Genomic variation in seven Khoe-San groups reveals adaptation and complex African history." Science. 2012, 338: 374-379.

It is also possible that Soweto Bantus are very genetically distinct from Mozambique Bantus and may be more similar to ancestral East African Bantus than modern East African Bantus, because they may lack subsequent Nilo-Saharan Ancestry and may, in general have less of a substrate influence.

The abstract of the paper and its citation data are as follows:

Malagasy genetic diversity results from an exceptional proto-globalisation process that took place over a thousand years ago across the Indian Ocean. Previous efforts to locate the Asian origin of Malagasy highlighted Borneo broadly as a potential source, but so far no firm source populations were identified. Here, we have generated genome-wide data from two Southeast Borneo populations, the Banjar and the Ngaju, together with published data from populations across the Indian Ocean region. We find strong support for an origin of the Asian ancestry of Malagasy among the Banjar. This group emerged from the long-standing presence of a Malay Empire trading post in Southeast Borneo, which favoured admixture between the Malay and an autochthonous Borneo group, the Ma’anyan. Reconciling genetic, historical and linguistic data, we show that the Banjar, in Malay-led voyages, were the most probable Asian source among the analysed groups in the founding of the Malagasy gene pool.

Brucatol, et al., "Malagasy genetic ancestry comes from an historical Malay trading post in Southeast Borneo." 33 (7) Molecular Biology and Evolution (July 5, 2016).

The literature cited is as follows (and admittedly includes some other papers I haven't yet seen):

* Adelaar A. 2009a. Towards an Integrated Theory about the lndonesian Migrations to Madagascar. In. Ancient human migrations: a multidisciplinary approach.: University of Utah Press

* Adelaar KA. 1995. Borneo as a cross-roads for comparative Austronesian linguistics. In: Canberra AAEP, editor. The Austronesians: historical and comparative perspectives. p. 81–102.

* Adelaar KA. 2009b. Loanwords in Malagasy. In: Haspelmath M, Tadmor U, editors. Loanwords in the world’s languages: a comparative handbook. Berlin, Germany: De Gruyter Mouton. p. 717-746.

* Adelaar KA 1989. Malay influence on Malagasy: linguistic and culture-historical implications. Oceanic Linguistics 28: 1-46. doi: 10.2307/3622973

* Adelaar KA. forthcoming. Who were the first Malagasy, and what did they speak? In: Acri A, Landmann A, editors. Cultural Transfer in Early Monsoon Asia. Singapore: Institute of Southeast Asian Studies.

* Alexander DH, Novembre J, Lange K 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19: 1655-1664. doi: 10.1101/gr.094052.109 by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from Beaujard P. 2012a. Les mondes de l’ocean indien. Vol. 2 : L’océan Indien, au cœur des globalisations de l'Ancien Monde (7e-15e siècles). Paris, France: Armand Collin. Beaujard P. 2012b. Les mondes de l’océan Indien. Vol. 1 : De la formation de l’État au premier système-monde afro-eurasien (4e millénaire av. J.-C.-6e siècle apr. J.-C.). Paris, France:

* Armand Collin. Brisbin A, Bryc K, Byrnes J, Zakharia F, Omberg L, Degenhardt J, Reynolds A, Ostrer H, Mezey JG, Bustamante CD 2012. PCAdmix: Principal componentsbased assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations. Human Biology 84: 343-364. doi: 10.3378/027.084.0401

* Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut F-X, Razafindrazaka H, Rakotondrabe AB, Ratolojanahary MA, Randriamarolaza L-P, Champion B, Dugoujon J-M 2013. Tracing arab-islamic inheritance in Madagascar: Study of the Y-chromosome and mitochondrial DNA in the Antemoro. PLoS One 8: e80932. doi: 10.1371/journal.pone.0080932

* Cox MP, Nelson MG, Tumonggor MK, Ricaut F-X, Sudoyo H 2012. A small cohort of Island Southeast Asian women founded Madagascar. Proceedings of the Royal Society B: Biological Sciences 279: 2761-2768. doi: 10.1098/rspb.2012.0012

* Dahl OC 1951. Malgache et maanjan: une comparaison linguistique. Oslo, Norway: Edege-Intituttet.

* Dahl OC 1991. Migration from Kalimantan to Madagascar. Oslo, Norway: Norwegian University Press : Institute for Comparative Research in Human Culture.

* Dewar RE, Wright HT 1993. The culture history of Madagascar. Journal of World Prehistory 7: 417-466. doi: 10.1007/BF00997802 by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from Fourquet R, Sarthou J, Roux J, Aori K 1974. Hemoglobine S et origines du peuplement de Madagascar: nouvelle hypothese sur son introduction en Afrique [Hemoglobin S and origins for the settlement of Madagascar: new hypothesis on its introduction to Africa]. Arch. Inst. Pasteur Madagascar 43: 185–220.

* Fuller DQ, Boivin N, Hoogervorst T, Allaby R 2011. Across the Indian Ocean: the prehistoric movement of plants and animals. Antiquity 85: 544-558.

* Hellenthal G, Busby GB, Band G, Wilson JF, Capelli C, Falush D, Myers S 2014. A genetic atlas of human admixture history. Science 343: 747-751. doi: 10.1126/science.1243518

* Hewitt R, Krause A, Goldman A, Campbell G, Jenkins T 1996. beta-globin haplotype analysis suggests that a major source of Malagasy ancestry is derived from Bantu-speaking Negroids. Am. J. Hum. Genet. 58: 1303–1308.

* Huffman TN. 2000. Mapungubwe and the origins of the Zimbabwe culture. In: Leslie M, Maggs T, editors. African naissance: The Limpopo valley 1000 years ago. Cape Town, South Africa: South African Archaeological Society. p. 14-29.

* Hurles ME, Sykes BC, Jobling MA, Forster P 2005. The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineages. Am J Hum Genet 76: 894-901.

* Kusuma P, Brucato N, Cox MP, Pierron D, Razafindrazaka H, Adelaar A, Sudoyo H, Letellier T, Ricaut F-X 2016. Contrasting Linguistic and Genetic Influences during the Austronesian Settlement of Madagascar. Scientific Reports 6:26066. doi: doi: 10.1038/srep26066

* Kusuma P, Cox MP, Pierron D, Razafindrazaka H, Brucato N, Tonasso L, Suryadi HL, Letellier T, Sudoyo H, Ricaut F-X 2015. Mitochondrial DNA and the Y by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics 16: 191. doi: 10.1186/s12864-015-1394-7

* Lawler A 2014. Sailing Sinbad's seas. Science 344: 1440-1445. doi: 10.1126/science.344.6191.1440

* Lawson DJ, Hellenthal G, Myers S, Falush D 2012. Inference of population structure using dense haplotype data. PLoS Genet 8: e1002453. doi: 10.1371/journal.pgen.1002453

* Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B 2013. Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193: 1233-1254. doi: 10.1534/genetics.112.147330

* Patterson N, Price AL, Reich D 2006. Population structure and eigenanalysis. PLoS Genet 2: e190. doi: 10.1371/journal.pgen.0020190

* Patterson NJ, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D 2012. Ancient admixture in human history. Genetics 192: 1065-1093. doi: 10.1534/genetics.112.145037

* Pickrell JK, Pritchard JK 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8: e1002967. doi: 10.1371/journal.pgen.1002967

* Pierron D, Razafindrazaka H, Pagani L, Ricaut F-X, Antao T, Capredon M, Sambo C, Radimilahy C, Rakotoarisoa J-A, Blench RM, Letellier T, Kivisild T 2014. Genome-wide evidence of Austronesian–Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar. Proceedings of the National Academy of Sciences 111: 936-941. doi: 10.1073/pnas.1321860111

* Ras JJ. 1968. Hikajat Banjar: a study in Malay historiography. The Hague: Martinus Nijhoff. by guest on July 12, 2016 http://mbe.oxfordjournals.org/ Downloaded from Serva M, Petroni F, Volchenkov D, Wichmann Sr 2012. Malagasy dialects and the peopling of Madagascar. Journal of the Royal Society Interface 9: 54-67. doi: 10.1098/rsif.2011.0228

* Soodyall H, Jenkins T, Hewitt R, Krause A, Stoneking M. 1996. The peopling of Madagascar. In: Boyce A, Mascie-Taylor C, editors. Molecular biology and human diversity. Cambridge, UK: Cambridge University Press. p. 156–170.

* Tofanelli S, Bertoncini S, Castri L, Luiselli D, Calafell F, Donati G, Paoli G 2009. On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages. Mol Biol Evol 26: 2109-2124.

Newcomers Transformed Madagascar From Jungle To Grassland 1000 Years Ago

[A]round 1,000 years ago, both stalagmites' calcium carbonate composition shifted suddenly and completely, from carbon isotope ratios typical of trees and shrubs, to those more consistent with grassland, within just 100 years.

From here.

The paper is Stephen J. Burns, et al., "Rapid human-induced landscape transformation in Madagascar at the end of the first millennium of the Common Era.", Quaternary Science Reviews (2016).

UPDATE March 2,  2016: The abstract to the paper reveals that the dates are actually a bit earlier than 1,000 years ago, which helps to reconcile the archaeological record which favors a date somewhat earlier than 1000 CE for Austronesian arrival in Madagascar and this new data point.  The abstract states:

The environmental impact of the early human inhabitants of Madagascar remains heavily debated. We present results from a study using two stalagmites collected from Anjohibe Cave in northwestern Madagascar to investigate the paleoecology and paleoclimate of northwestern Madagascar over the past 1800 years. Carbon stable isotopic data indicate a rapid, complete transformation from a flora dominated by C3 plants to a C4 grassland system. This transformation is well replicated in both stalagmites, occurred at 890 CE and was completed within one century. We infer that the change was the result of a dramatic increase in the use of fire to promote the growth of grass for cattle fodder. Further, stalagmite oxygen isotope ratios show no significant variation across the carbon isotope excursion, demonstrating that the landscape transformation was not related to changes in precipitation. Our study illustrates the profound impact early inhabitants had on the environment, and implies that forest loss was one trigger of megafaunal extinction.

It also isn't implausible to think that the use of fire to cover forest to grassland wouldn't have begun immediately upon their arrival.  They would have used the modest amount of existing grassland on the island at first and would have cleared more land only after their growing herds strained the carrying capacity of the existing grasslands.

Rethinking Madagascar's Prehistory

There are archaeological traces of villages of mixed Indonesian and East African heritage dating back to at least 500 CE in Madagascar, a date that roughly coincides with megafauna extinctions on the island.[1]  The Malagasy language spoken in Madagascar is closely related to a particular Austronesian language spoken in a particular river valley of Borneo from which about 90% of the words in Malagasy are derived.[5]  The remaining Malagasy lexicon is derived from a number of other Southeast Asian and South Asian languages, and from the African Bantu language.[5]

Linguistic and cultural evidence, strongly supported by archaeological evidence, population genetic evidence, evidence of Indonesian plants that appeared in Africa with Austronesian names around that time (e.g. the banana is native to Southeast Asia, not to Africa), and evidence of Austronesian seamanship in Oceania that make such a journey plausible, all combine to make the settlement of Madagascar one of the most well established and remarkable long distance migrations of a whole people in pre-modern human history.

The story from the genetic evidence

A number of studies have been done of the non-recombining Y-DNA population genetics, mtDNA population genetics, and autosomal population genetics of the Malagasy people.[2][3][4][5][6][7][8].  These studies show significant (but differing) relative proportions of Asian and African genetic origins in Y-DNA, mtDNA, and autosomal DNA.  Only a small portion of Malagasy individuals are entirely Asian or entirely African as measured by their Y-DNA, mtDNA and autosomal DNA.[3]  The vast majority of the Asian genetic contribution to this population is consistent with origins in Southern Borneo.[2][4][5][6]  Based on the mtDNA diversity in the Asian part of the mtDNA of the Malagasy people, it is estimated that there were only about thirty women in the Indonesian founding population of the island.[6]

The African component of the population genetic makeup of the Malagasy people is a better match, in Y-DNA, mtDNA and autosomal genetics, to East African Bantus, such as the Luhya people, than to any other modern African population.

The African component of the uniparental and autosomal components of Malagasy population genetics.  As a percentage of the total mtDNA mix in the Malagasy population, the African haplogroup breakdown in one study was as follows [5]:
L* 5%
L2b1b 2%
L3b1 28%
L3e1a 4%
Total: 37%
Asian: 63%

Of these mtDNA haplogroups, all are very typical of Bantu populations except L* (which may in this context mean L not elsewhere classified rather than maximally basal form of haplogroup L).[12]

As a percentage of the total Y-DNA mix in the Malagasy population, the African haplogroup breakdown was comprised mostly of E3a (36% of the total), with smaller amounts of E2b, E1b1a, and B2.[5] These are mostly characteristic Bantu Y-DNA haplogroups.[11]

Genetics blogger Razib Khan compared the whole genomes of two Malagasy individuals to a number of reference populations.[8][9]  He used software that does a best fit of the data from the reference populations and subjects to ten hypothetical source populations using what amounts to eigenvector analysis of the data sets.  With this software, he was able to estimate the percentage of the African component in the Malagasy individuals attributable to each of the source populations, and to compare the mix of African autosomal genetic components in these individuals to those in his African reference populations.

The largest African component in each Malagasy individual was a component which makes up about 90% to 95% of the Mandenka and Yoruba populations, which a Bantu peoples from near the Nigeria-Cameroon border where the Bantu people originated.  There was also small contributions of from other African autosomal genetic components:

*About 3-4% (of the total) of a component that is modal in the pastoralist Nilo-Saharan Maasi of East Africa and in Ethiopian Jews.  This contribution made up about the same share of the African autosomal genetics of both Malagasy individuals, but in each case was smaller relative to the Bantu contribution than in the East African Bantu Luhya reference population.

*About 2-4% (of the total) of the various components that are predominant in Biaka Pygmies, Mbuti Pygmies, the San people, and the Sandawe people of Africa (all of whom are relict hunter-gatherer populations in Africa).  The proportion of these components in the Malagasy individuals relative to the size of their Bantu genetic component was very similar to that seen in the East African Bantu Luhya reference population.

*There was no evidence of admixed contributions from Yemen Jews (a SW Asian reference population) or a European reference population, although there were both SE Asian and South Asian autosomal components of the Asian part of their autosomal genetics.

In sum, Razib Khan's detailed, nuts and bolts autosomal genetic analysis of Malagasy individuals shows that the African contribution to their autosomal DNA looks very much like that of East African Bantu Luhya people, except that the East African Bantus show more Nilo-Saharan admixture.

History may explain the discrepancy.  It is likely that a group of Africans joined a group of Borneans with some minor South Asian admixture to make the trip to Madagascar and settled there at around this earliest archaeologically supported data for an Indonesian presence in Madagascar around 500 CE.  There is historical and prehistory evidence (including Maasai oral histories) to suggest that  the Maasai people and other Nilo-Saharan peoples migrated through East Africa from North to South starting around the 1400s CE.  If this contact resulted in some level of admixture in the hundred of years between then and the present, we would expect modern East African Bantus to have more Nilo-Saharan admixture today than they did in the 500s CE at the time of the fusional proto-Malay ethnogenesis.

Other autosomal genetic studies of the Malagasy people have likewise concluded that the African component of the Malagasy autosomal gene pool is basically Bantu in character.[2][3]  And, the uniparental genetic studies have similarly been congruent with a predominantly East African Bantu source for the African component of the Malagasy gene pool.[3][4][5]

Notably, the only study of which I am aware of the autosomal population genetics of Mozambique, the Southeastern African country closest to the island of Madagascar specifically noted that the Bantu people of Mozambique are not genetically similar to any of the three reference populations that Razib Khan compared to the two Malagasy individuals for whom he had whole genome data:  the Mandenka and Yoruba populations, and the East African Bantu Luhya people.[9] The population genetics of the Bantus of Mozambique show far less population replacement and far more assimilation of an indigenous pre-Bantu population that is genetically distant from any of the extant relict hunter-gather "Paleo-African" populations of Africa that are extant today.[9]

The studies of autosomal genetics in Madagascar that have been done to date either showed no sign at all of a Mozambique component to the gene pool of the Malagasy people,[2][7][8], although one uniparental study did see some sign of a trace and secondary contribution of Mozambique or the vicinity.[5]  That 2009 high resolution uniparental genetics study stated:

The pattern of diffusion of uniparental lineages was compatible with at least two events: a primary admixture of proto-Malay people with Bantu speakers bearing a western-like pool of haplotypes, followed by a secondary flow of Southeastern Bantu speakers unpaired for gender (mainly male driven) and geography (mainly coastal).

Thus, a small number of Malagasy people have Y-DNA haplotypes associated with coastal Mozambique or the vicinity, and an even smaller number of individuals have mtDNA haplogroups that are distinctively from there.

The new evidence

A study released this summer complicates this neat and simple narrative.

The new study finds clearly modern human microlithic stone tools and other artifacts in layers of two long occupied terrestrial forager villages in Madagascar dating back to about 2000 BCE, about 2500 years before the earliest solid evidence of proto-Malagasy settlement in Madagascar.[1]  These settlements also greatly predate the megafauna extinctions that occurred in Madagascar when the mix of Borneans and East African Bantus who gave rise to the Malagasy people arrived.[1]

This first wave of settlers must have been either entirely replaced or swamped demographically by the proto-Malay people who arrived around 500 CE. The people who were in the first wave of human settlers of Madagascar could not have been Bantus, because the Bantu expansion, which began about 2000 BCE in West Africa near the Nigeria-Cameroon border, did not reach the East African coast until ca. 1000 BCE.[10]  But, the African genetic component of the Malagasy people is East African Bantu which is very different from that of all coastal populations of Africa around 2000 BCE, so this genetic contribution to the Malagasy people must have arrived later, probably in the same boats that the Austronesians did.  The absence of non-Eastern Bantu genes in the Malagasy gene pool, establishes that these indigenous foragers of Madagascar did not contribute much to the modern gene pool, either because they were entirely replaced, or because their contribution was so small in proportion to the newcomers that it has left almost no discernible mark on the modern gene pool in Madagascar.

Alternatively, the foragers could have been relocated to continental Africa by the Austronesians, in a manner similar to the relocation of Native Americans to reservations in early American history, although this seems like a possibility with fewer historical precedents in the expansion histories of the Austronesian and Bantu peoples who made up the proto-Malays.

The data interpreted as a subsequent and secondary wave of male dominated migration from Mozambique in the high resolution uniparental genetic data [5] could really be, at least in part, a relict of pre-Malay African foragers in Madagascar.  But, the fact that the Southeast African uniparental genetic haplogroups are male dominated disfavors a relict population as the primary source of these Southeast African uniparental genetic haplogroups in the Malagasy gene pool.  Generally, when an indigenous substrate population is demographically swamped by a newly arrived dominant superstrate population, more matriline transmitted mtDNA survives in the resulting gene pool from the substate population than Y-DNA.

So, the maximum contribution of a relict population to the Malagasy gene pool is probably some fraction of the distinctively Southeast African contribution that was observed in [5] and the data are not inconsistent with a total replacement of the first wave humans of Madagascar by the proto-Malays that left no surviving genetic trace of this first wave forager population (i.e. with genocide).

Why didn't first wave human settlers of Madagascar cause a mega-fauna extinction?

Equally important, why didn't the arrival of African foragers ca. 2000 BCE result in a mega-fauna extinction in Madagascar as hunter-gatherer migrations into Australia and Papua New Guinea, into the Americas, in Europe and into Siberia did tens of thousands of years earlier with presumably more primitive technology?

This is also not a case comparable to that of continental Africa where the local wildlife co-evolved with modern humans and their hominin predecessors and hence learned to survive in spite of them for tens of thousands of years.

How could this be possible?

Here is one speculative narrative that could explain this new discovery.

The arrival of this first wave of African foragers may have been a one way trip by a small population made possible only by luck and pluck that wasn't repeated.  If these foragers had been able to reliably navigate to Madagascar and back at the time, presumably, they would have engaged in trade with mainland Africa.  But, there is no archaeological evidence of ongoing trade between Madagascar and continental African prior to 500 CE, which would have been highly distinctive in the archaeological record because it contained species of flora and fauna found nowhere in mainland Africa.

In a case similar to that of the people of Tasmania, once separated from their continental African communities, they may have regressed technologically (e.g. in terms of hunting effectiveness) as their population fell below critical mass to sustain this knowledge, if not immediately, after some mishap or bad foraging season or disease outbreak at a latter time.  They may have held on to enough cultural capital to be a sustainable population, but may not have been a large enough community to sustain the level of excellence in hunting and gathering practices that made them a dominant species in Africa and Eurasia and the Americas.

Since Madagascar's flora and fauna are so distinct from those of continental Africa, it may also have been the case in which the knowledge the first wave African foragers brought with them from continental Africa may have been of limited usefulness in this new ecology. Since they were not farmers or herders, they would have brought no familiar plants or animals to feed themselves with them.  The need to rapidly develop new gathering skill sets could have given this first wave of modern humans on the island a rocky start, causing their population to fall before eventually recovering as they learned to adapt to local conditions.  This could have caused them to regress culturally, in part from their loss of important hunting and gathering knowledge. Without the cultural capital shared by other Upper Paleolithic peoples who brought about mega-fauna extinctions (and contributed to the demise of the Neanderthals), they may have lost the capacity to become so dominant as hunters and gatherers who could cause mega-fauna extinctions.

There also isn't even any sign that they brought domesticated dogs with them.  Dogs were first domesticated around 30,000 years ago and were widespread by ca. 2000 BCE, even into Australia where they weren't initially present for tens of thousands of years but appeared about 4000 years ago. Perhaps the relevance of domesticated dogs that modern humans brought with them has been underestimated, which could also explain why Southeast Asia, which is a point of origin of many species of domestic dogs, has so less mega-fauna extinction since Southeast Asian fauna co-evolved with these dogs.

Even if the first wave of humans in Madagascar eventually recovered technologically and cultural, centuries later, their recovery may have been gradual enough to be less disruptive to the local ecology.

These disadvantages wouldn't burden later proto-Malays who brought food sources with them, had reliable sea transportation that permitted them to colonize Madagascar at populations in excess of the critical mass needed to sustain their population, and thus didn't need detailed knowledge of how to turn indigenous plants and animals into food and didn't suffer the cultural regression that may have been experienced by first wave foragers on the island twenty-five centuries earlier.

References

1. Robert E. Deward et al., "Stone tools and foraging in northern Madagascar challenge Holocene extinction models.", PNAS (2013).[doi:10.1073/pnas.1306100110] (Mr. Deward died on April 8, 2013.)

2. Regueiro, et al., "Austronesian genetic signature in East African Madagascar and Polynesia.", Journal of Human Genetics (2008) 53, 106–120; doi:10.1007/s10038-007-0224-4

3. Poetsch, et al., "Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example.", European Journal of Human Genetics (24 April 2013) doi:10.1038/ejhg.2013.51

4. Hurles, et al. "The dual origin of the malagasy in island southeast Asia and East Africa: evidence from maternal and paternal lineages.", Am J Hum Genet. 2005;76;894-901. PMID: 15793703

5. Tofanelli, et al., "On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages.", Mol. Biol. Evol. 26, 2109–2124 (2009) (doi:10.1093/molbev/msp120)

6. Cox, et al., "A small cohort of Island Southeast Asian women founded Madagascar", Proc. R. Soc. B. (21 March 2012) doi: 10.1098/rspb.2012.0012

7. Razib Khan, "The Betsileo of Madagascar are Malay and Bantu.", Gene Expression (October 23, 2011). (Supplemental materials: here).

8. Razib Khan, "The Merina of Madagascar are Malay and Bantu.", Gene Expression (September 9, 2011).

9. Sikora, et al., "A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations.", European Journal of Human Genetics (2011) 19, 84–88; doi:10.1038/ejhg.2010.141.

10.  Wikipedia entry on "Bantu Expansion" (the Bantu reach the East African coast sometime after 1500 BCE and before 500 BCE; and there is no evidence of Bantu seafaring activity independent of assistance from other cultures such as the Austronesians).

11.  Gemma Berniell-Lee, et al., "Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages.", Molecular Biology and Evolution (April 2009) doi:10.1093/molbev/msp069 (quoted at Dienekes' Anthropology Blog)("these lineages have been associated either to Bantu-speaking people - E1b1a (E3a according to The Y Chromosome Consortium (2002)), B2a, and E2 - or to Pygmy populations (haplogroup B2b).").

12.  Salas, et al., "The Making of the African mtDNA Landscape",  Am J Hum Genet. 71(5): 1082–1111.(November 2002) PMCID: PMC385086. ("L2b, L2c, and L2d appear to be largely confined to West and western Central Africa (and African Americans), with only minor occurrences of a few derived types in the southeast. . . . [L3b is a] major southeastern haplogroups of clear West African origin. . . .  L3e1 is distributed throughout sub-Saharan Africa, but it is especially common in southeastern Africa. This clade appears to have a west Central African origin and is rare among West Africans, although it is well represented among African Americans. Several southeastern African types are shared with East African Bantu-speaking Kikuyu from Kenya. This suggests that L3e1 may have spread into Kenya via the eastern stream from a Cameroon source population (best represented in this data set by Bioko and São Tomé) or from some Central African source. It subsequently dispersed into the southeast (although, with so little data, back migration into Kenya cannot be ruled out). The African American types may be the result of direct transportation from Mozambique, given the lack of West African representatives. One L3e1a type is also present at elevated frequency in the Khwe, but, since it matches two Herero and also has a direct derivative in the southeast, this again appears to have been the result of gene flow from Bantu speakers, even though the type has not been sampled in that group.")