Fairies And Fungi

* Fairy rings are a fungal phenomena.

* Fairies are often depicted as chthonic with underground halls, and eating fairy food traps you in their world forever. Fungi are one of the few living things that can survive and thrive underground without light.

* The Santa Claus myth and Christmas tree ornaments are deeply tied to hallucinogenic mushroom use by shamans in places where reindeer roam.

* Fungi are pervasively present in temperate forests which are seen as a natural habitat of fairies and were places feared in medieval times.

* Fairies are associated with glamours and deception, and many fungi, such as ergot, cause hallucinations and a sense of distortion of time..

* Fungal infections can make insects and small plants look and behave weirdly in ways that could cause them to be called fairies.

* The bane of fairies, iron and to a lesser degree salt, are inorganic while fungi are organic.

* Curious children eating mushrooms that cause their death or cause them to act abnormally could be associated with the changling myth.

* Fungi come in many varieties that are hard to distinguish from each other like fungi.

* Fungi have properties that distinguish them from "normal" biological things like plants and animals.

* Could "fairy dust" be spores or yeast?

* Mushrooms are of a scale often associated with fairies.

* There is a forests, fairies, and fungi sticker book anthology.

* Fairies are often depicted as amoral or having fundamentally different motivations than humans, which is a fit to fungi and its effects on mankind.

Humans In African Jungles 150,000 Years Ago

Modern humans existed in wet tropical forests of West Africa about 150,000 years ago, contrary to the believe that humans could only survive in this kind of ecological environment through trade with farmers.

Humans emerged across Africa shortly before 300 thousand years ago (ka). Although this pan-African evolutionary process implicates diverse environments in the human story, the role of tropical forests remains poorly understood. 

Here we report a clear association between late Middle Pleistocene material culture and a wet tropical forest in southern Côte d’Ivoire, a region of present-day rainforest. Twinned optically stimulated luminescence and electron spin resonance dating methods constrain the onset of human occupations at Bété I to around 150 ka, linking them with Homo sapiens. Plant wax biomarker, stable isotope, phytolith and pollen analyses of associated sediments all point to a wet forest environment. 

The results represent the oldest yet known clear association between humans and this habitat type. The secure attribution of stone tool assemblages with the wet forest environment demonstrates that Africa’s forests were not a major ecological barrier for H. sapiens as early as around 150 ka.

Eslem Ben Arous, et al.,"Humans in Africa’s wet tropical forests 150 thousand years ago" Nature (February 26, 2025).

A Long, Long Time Ago, On Earth

 The names are obviously anachronistic.

Borgs

Scientists last year discovered a whole new kind of DNA bearing entity. Whether it is an organism itself isn't entirely clear, and if it is one, it doesn't fit into any of the existing categories of DNA bearing entities.

It's one thing to find a new species or even a new family or organisms, it's another to find a whole new kind of organism which is on a par with being the first person to discover viruses. It is quite an exciting discovery.

In the TV series Star Trek, the Borg are cybernetic aliens that assimilate humans and other creatures as a means of achieving perfection. So when Jill Banfield, a geomicrobiologist at the University of California, Berkeley, sifted through DNA in the mud of her backyard and discovered a strange linear chromosome that included genes from a variety of microbes, her Trekkie son proposed naming it after the sci-fi aliens. The new type of genetic material was a mystery. Maybe it was part of a viral genome. Maybe it was a strange bacterium. Or maybe it was just an independent piece of DNA existing outside of cells. . . .

Banfield . . . and graduate student Basem Al-Shayeb were searching for viruses that infect archaea, a type of microbe often found in places devoid of oxygen. They would dig 1 meter or more below the surface and collect mud samples that might harbor archaea and their viruses. Next, they would sequence every stretch of DNA in the samples and use sophisticated computer programs to scan for sequences that signified a virus, rather than any other organism.

"We started off with a piece of mud and 10 trillion pieces of DNA," Banfield says. One sample, taken from the mud on her property, contained a gene-filled stretch of DNA almost 1 million bases long—and more than half the genes were novel. This linear stretch of DNA also had a particular pattern of bases at its beginning and end, distinct stretches of repetitive DNA between its genes, and two places along the sequence where DNA duplication could begin—which indicated the Borg could make copies of itself. Together, this suggested it was not just a random concoction of genes.

After they identified the first Borg sequence, the researchers began to scan microbial DNA in public databases to see whether they could find anything similar. They found a few variations in groundwater from Colorado—there, the first purported Borg showed up about 1 meter deep and got more abundant deeper down. Other versions showed up in DNA from the discharge of an abandoned mercury mine in Napa, California, and from a shallow riverbed of the East River in Colorado.

Altogether, the researchers isolated 23 sequences they think may be Borgs—and 19 they have identified as having all the characteristics of the first Borg they discovered, they write . . . on the preprint server bioRxiv. Some are almost 1 million bases long. "I don't think anything else that's been discovered is as big as these guys are," among previously known extrachromosomal DNA elements, Doolittle says.

In every place, copies of the Borg co-occurred with DNA linked to a methane-oxidizing archaeon called Methanoperedens. That suggests the Borgs may exist inside the microbe, the researchers say. But because Methanoperedens can't be grown in a lab, the team hasn't been able to confirm this suspicion. Meanwhile, team members have ruled out the possibility that the Borg came from another microbe, as they lack many necessary genes for life, or a virus, which typically have shorter chromosomes.

From Science.

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions, yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetland soil where methane production and oxidation occur, we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins. Four curated, complete genomes are linear, up to ~1 Mbp in length and share genome organization, including replicore structure, long inverted terminal repeats, and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are a new type of archaeal extrachromosomal element with a distinct evolutionary origin. Gene sequence similarity, phylogeny, and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as “Borgs”. We identified at least 19 different Borg types coexisting with Methanoperedens in four distinct ecosystems. Borg genes expand redox and respiratory capacity (e.g., clusters of multiheme cytochromes), ability to respond to changing environmental conditions, and likely augment Methanoperedens capacity for methane oxidation (e.g., methyl coenzyme M reductase). By this process, Borgs could play a previously unrecognized role in controlling greenhouse gas emissions.

Basem Al-Shayeb, "Borgs are giant extrachromosomal elements with the potential to augment methane oxidation" bioRxiv (July 10, 2021).

Troödons

Troödons are currently my favorite dinosaur. But for the extraterrestrial impact that wiped out the dinosaurs in the Gulf of Mexico about 65 million years ago, they would have been top candidates to become the dominant intelligent species on Earth.

A Troödon "is a large-brained nocturnal Troodontid theropod, which lived in the latter part of the Cretaceous period. It . . . may have had camouflage markings on its hide, to help it catch the nocturnal mammals which formed a small part of its diet. . . . it was also feathered. Troodon had abnormally large eyes, and these helped Troodon to see after the setting of the sun . . . . Troodon . . . is generally accepted as having been . . . warm - blooded. . . . It lived in what is now North America during the late Cretaceous Period (100-65 mya) and grew to be about 8 feet to 10 feet long and about 110 lbs. in weight. This slender little dinosaur might be the most intelligent dinosaur ever to exist. Troodon ate mammals, small dinosaurs, eggs and juvenile Hadrosaurs. It also specializes in pack hunting to hunt bigger prey.

From the Dinosaur Wiki. 

The Ecological Impact Of Adolescent T-Rex Type Dinosaurs

There are small predator dinosaurs and huge predator dinosaurs (1000 kg to 8000 kg), but none with adult sizes between 100 kg and 1000 kg. 

Why?

Because that ecological gap was filled by adolescent dinosaurs that are the size of house cases when born but grow to the size of a city bus as an adult.

Because they were born from eggs, dinosaurs like T. rex necessarily were born small -- about the size of a house cat. This meant as they grew to the size of a city bus, these "megatheropods," weighing between one and eight tons, would have changed their hunting patterns and prey items. It's long been suspected by paleontologists that giant carnivorous dinosaurs would change behavior as they grew. But how that might have affected the world around them remained largely unknown.

"We wanted to test the idea that dinosaurs might be taking on the role of multiple species as they grew, limiting the number of actual species that could co-exist in a community," said Schroeder.

The number of different types of dinosaurs known from around the globe is low, particularly among small species.

"Dinosaurs had surprisingly low diversity. Even accounting for fossilization biases, there just really weren't that many dinosaur species," said Felisa Smith, professor of Biology at UNM and Schroeder's graduate advisor.

To approach the question of decreased dinosaur diversity, Schroeder and her coauthors collected data from well-known fossil localities from around the globe, including over 550 dinosaur species. Organizing dinosaurs by mass and diet, they examined the number of small, medium and large dinosaurs in each community.

They found a strikingly clear pattern:

"There is a gap -- very few carnivorous dinosaurs between 100-1000kg [200 pounds to one ton] exist in communities that have megatheropods," Schroeder said. "And the juveniles of those megatheropods fit right into that space."

Schroeder also notes that looking at dinosaur diversity through time was key. Jurassic communities (200-145 million years ago) had smaller gaps and Cretaceous communities (145-65 million years ago) had large ones.

"Jurassic megatheropods don't change as much -- the teenagers are more like the adults, which leaves more room in the community for multiple families of megatheropods as well as some smaller carnivores," Schroeder explained. "The Cretaceous, on the other hand, is completely dominated by Tyrannosaurs and Abelisaurs, which change a lot as they grow."

To tell whether the gap was really caused by juvenile megatheropods, Schroeder and her colleagues rebuilt communities with the teens taken into account. By combining growth rates from lines found in cross-sections of bones, and the number of infant dinosaurs surviving each year based on fossil mass-death assemblages, the team calculated what proportion of a megatheropod species would have been juveniles.

Schroeder explained that this research is important because it (at least partially) elucidates why dinosaur diversity was lower than expected based on other fossil groups. It also explains why there are many more very large species of dinosaurs than small, which is the opposite of what would be expected. But most importantly, she added, it demonstrates the results of growth from very small infants to very large adults on an ecosystem.

From Science Daily. The paper with its significance statement and abstract are as follows:

Not enough room

Modern carnivore communities include species that span a range of body sizes. For example, on the African savannah, there are small species (mongooses), medium species (wild dogs), and large species (lions). This variation reflects available prey sources that best suit each group. Carnivorous dinosaur communities, however, were missing species that fall into the middle, or mesocarnivore, group as adults. Schroeder et al. looked across communities, space, and time and found that this absence appears to have been driven by the distinctive biology of dinosaurs, in which giant adults start out as tiny hatchlings. Growing juvenile dinosaurs thus filled the other niches and limited trophic species diversity.

Abstract

Despite dominating biodiversity in the Mesozoic, dinosaurs were not speciose. Oviparity constrained even gigantic dinosaurs to less than 15 kg at birth; growth through multiple morphologies led to the consumption of different resources at each stage. Such disparity between neonates and adults could have influenced the structure and diversity of dinosaur communities. Here, we quantified this effect for 43 communities across 136 million years and seven continents. We found that megatheropods (more than 1000 kg) such as tyrannosaurs had specific effects on dinosaur community structure. Although herbivores spanned the body size range, communities with megatheropods lacked carnivores weighing 100 to 1000 kg. We demonstrate that juvenile megatheropods likely filled the mesocarnivore niche, resulting in reduced overall taxonomic diversity. The consistency of this pattern suggests that ontogenetic niche shift was an important factor in generating dinosaur community structure and diversity.

Katlin Schroeder, S. Kathleen Lyons, Felisa A. Smith. "The influence of juvenile dinosaurs on community structure and diversity." 371 (6532) Science 941 (2021). DOI: 10.1126/science.abd9220

Paleo-Americans?

It is no secret that I have long been on skeptical side of the debate around whether modern humans were present in the Americas outside the Beringian land bridge between Siberia and Alaska until the tail of of the ice age that produced the Last Glacial Maximum about 26,000 years ago. The pre-Clovis arrival of members of the Founding population of the Americas to North and South America via a Pacific route became part of the paradigm long ago. 

But evidence of a hominin presence in the Americas during or before the Last Glacial Maximum ice age has relied on very small numbers of objects that are only arguably stone tools at various sites, with equivocal attempts at dating them, and no human remains. 

Two new articles in the leading scientific journal Nature may tip the balance, although I am still not unequivocally convinced, in part, because the studies fail to address by this pilot wave founding population would have had so slight an archaeological and ecological impact.

An account at NBC News explains in an article that is mostly correct and makes only subtle errors where it is not quite right:

Pieces of limestone from a cave in Mexico may be the oldest human tools ever found in the Americas, and suggest people first entered the continent up to 33,000 years ago – much earlier than previously thought. 

The findings, published Wednesday in two papers in the journal Nature, which include the discovery of the stone tools, challenge the idea that people first entered North America on a land bridge between Siberia and Alaska and an ice-free corridor to the interior of the continent.

Precise archaeological dating of early human sites throughout North America, including the cave in Mexico, suggests instead that they may have entered along the Pacific coast, according to the research. . . . 

The commonly accepted time for the arrival of the first people in North America is about 16,000 years ago, and recent studies estimate it happened up to 18,000 years ago. But the latest discoveries push the date back by more than 10,000 years. 

The NBC article linked about says this about the first article discussing an excavation deep into a cave high on a mountain in Mexico: 

Ciprian Ardelean, an archaeologist with the Autonomous University of Zacatecas in Mexico, the lead author of one of the papers, said the finds were the result of years of careful digging at the Chiquihuite Cave in north-central Mexico. 

The steeply-inclined cave is high on a mountainside and filled with crumbling layers of gravel: “The deeper you go, the higher the risk for the walls to collapse,” he said. 

A shaped limestone point, one of the stone tools found at the Chiquihuite Cave in central Mexico that archaeologists think dates from around 30,000 years ago, before the last Ice Age.

The excavations paid off with the discovery of three deliberately-shaped pieces of limestone — a pointed stone and two cutting flakes — that may be the oldest human tools yet found in the Americas. 

They date from a time when the continent seems to have been occupied by only a few groups of early humans – perhaps “lost migrations” that left little trace on the landscape and in the genetic record, Ardelean said. 

The tools were found in the deepest layer of sediment they excavated, which dates from up to 33,000 years ago – long before the last Ice Age, which occurred between 26,000 and 19,000 years ago. . . . 

“You have to live there and cook there, because it takes you a whole day to go back and forth from the town, and it’s a five-hour climb,” he said. “It is a logistical nightmare.”

More tools were found in sediments laid down during and after the Ice Age, and indicate the cave was occupied for short periods over thousands of years, maybe by nomadic people who knew of it from ancestral legends. 

The Chiquihuite Cave is high on a mountain, at an altitude of above 8,800 feet, and the interior is very steep. . . . 

“I think it was a refuge used occasionally and periodically,” Ardelean said. “Even if you never saw the site before, your grandparents had told you about it and there were indications when you got there.” 

The presence of stone tools from the Ice Age – known to archaeologists as the Last Glacial Maximum, or LGM – suggested people occupied the cave even before that. 

Much of North America was then covered with thick ice sheets that would have made migrations impossible, he said: “If you have people during the LGM, it is because they entered the continent before the LGM.” 

The first article and its abstract are:

The initial colonization of the Americas remains a highly debated topic, and the exact timing of the first arrivals is unknown. The earliest archaeological record of Mexico—which holds a key geographical position in the Americas—is poorly known and understudied. Historically, the region has remained on the periphery of research focused on the first American populations. 

However, recent investigations provide reliable evidence of a human presence in the northwest region of Mexico, the Chiapas Highland, Central Mexico and the Caribbean coast, during the Late Pleistocene and Early Holocene epochs. Here we present results of recent excavations at Chiquihuite Cave—a high-altitude site in central-northern Mexico—that corroborate previous findings in the Americas of cultural evidence that dates to the Last Glacial Maximum (26,500–19,000 years ago), and which push back dates for human dispersal to the region possibly as early as 33,000–31,000 years ago. 

The site yielded about 1,900 stone artefacts within a 3-m-deep stratified sequence, revealing a previously unknown lithic industry that underwent only minor changes over millennia. More than 50 radiocarbon and luminescence dates provide chronological control, and genetic, palaeoenvironmental and chemical data document the changing environments in which the occupants lived. 

Our results provide new evidence for the antiquity of humans in the Americas, illustrate the cultural diversity of the earliest dispersal groups (which predate those of the Clovis culture) and open new directions of research.

Ardelean, C.F., Becerra-Valdivia, L., Pedersen, M.W. et al. "Evidence of human occupation in Mexico around the Last Glacial Maximum." Nature (July 22, 2020). https://doi.org/10.1038/s41586-020-2509-0 (citations in abstract omitted).

The NBC article linked about says this about the second article:  

Lorena Becerra-Valdivia, an archaeological scientist at the University of Oxford and the University of New South Wales, and Thomas Higham, a radiocarbon dating specialist at the University of Oxford, compared the dates from the cave sediments with other archaeological sites in North America. 

Their research indicates very small numbers of humans probably lived in parts of North America before, during and immediately after the last Ice Age, but the human population grew much larger after a period of abrupt global warming that began about 14,700 years ago. 

The study also suggested some people had entered the Americas before 29,000 years ago, possibly along the Pacific coast, when the land bridge between Siberia and Alaska was completely or partially submerged, Becerra-Valdivia said. . . . 

Anthropologist Matthew Des Lauriers of California State University, San Bernardino, who was not involved in the studies, said they “pushed the boundaries” of knowledge about the earliest human arrival in the Americas. 

But he questioned how ancient people who had been in the Americas for more than 25,000 years could have remained “archaeologically invisible” for over 10,000 years.

He said that archaeologists in Australia and Japan, for example, had no difficulty finding evidence of human occupation from that time. 

The second article and its abstract are: 

The peopling of the Americas marks a major expansion of humans across the planet. However, questions regarding the timing and mechanisms of this dispersal remain, and the previously accepted model (termed ‘Clovis-first’)—suggesting that the first inhabitants of the Americas were linked with the Clovis tradition, a complex marked by distinctive fluted lithic points—has been effectively refuted. 

Here we analyse chronometric data from 42 North American and Beringian archaeological sites using a Bayesian age modelling approach, and use the resulting chronological framework to elucidate spatiotemporal patterns of human dispersal. We then integrate these patterns with the available genetic and climatic evidence. 

The data obtained show that humans were probably present before, during and immediately after the Last Glacial Maximum (about 26.5–19 thousand years ago) but that more widespread occupation began during a period of abrupt warming, Greenland Interstadial 1 (about 14.7–12.9 thousand years before AD 2000). 

We also identify the near-synchronous commencement of Beringian, Clovis and Western Stemmed cultural traditions, and an overlap of each with the last dates for the appearance of now-extinct faunal genera. Our analysis suggests that the widespread expansion of humans through North America was a key factor in the extinction of large terrestrial mammals.

Lorena Becerra-Valdivia, Thomas Higham, "The timing and effect of the earliest human arrivals in North America" Nature (July 22, 2020) DOIhttps://doi.org/10.1038/s41586-020-2491-6 (citations in abstract ommitted).

Youngest Homo Erectus Remains Are About 100,000 Years Old

This reaffirms the paradigm and status quo, that Homo erectus had a million year run in Asia and vanished shortly (percentage-wise) before modern humans arrived.

Razib reminds us that there were many archaic hominin species in Asia contemporaneously with Homo erectus, including Neanderthals, Denisovans, the "hobbits" of Flores, and an additional species or three in the Philippines and possible China too. Modern humans reached Sumatra no later than 70,000 years ago, immediately after the Toba eruption.

It wouldn't be surprising to find new Homo erectus remains later, or new modern human remains earlier, that would narrow the gap between the two species or possible leave evidence of a brief overlap like the 1,000 years overlaps characteristic of Europe at a local level.

This species diversity may have flowed from topographies and ecologies that created many separate and independent ecological micro-niches that could not be sustained, for example, on a broad flat plain or in an area with thin trees cover and rolling hills.

My personal conjecture is that the Toba eruption resulted in temporary ecological changes that devastated the already low density H. erectus population and cleared the way for an influx of modern humans from South Asia via Myanmar. Modern humans eventually killed almost all of the stragglers, although relict populations of H. erectus may have survived many thousands or tens of thousands of years past first contact and I don't rule out the possibility that there is still a small relict population of archaic hominins or archaic hominin hybrids deep in some Indonesian jungle. If archaic hominins continue to exist anywhere, it is probably there.  

Homo erectus is the founding early hominin species of Island Southeast Asia, and reached Java (Indonesia) more than 1.5 million years ago. Twelve H. erectus calvaria (skull caps) and two tibiae (lower leg bones) were discovered from a bone bed located about 20 m above the Solo River at Ngandong (Central Java) between 1931 and 1933, and are of the youngest, most-advanced form of H. erectus. Despite the importance of the Ngandong fossils, the relationship between the fossils, terrace fill and ages have been heavily debated. 

Here, to resolve the age of the Ngandong evidence, we use Bayesian modelling of 52 radiometric age estimates to establish—to our knowledge—the first robust chronology at regional, valley and local scales. We used uranium-series dating of speleothems to constrain regional landscape evolution; luminescence, 40argon/39argon (40Ar/39Ar) and uranium-series dating to constrain the sequence of terrace evolution; and applied uranium-series and uranium series–electron-spin resonance (US–ESR) dating to non-human fossils to directly date our re-excavation of Ngandong.

We show that at least by 500 thousand years ago (ka) the Solo River was diverted into the Kendeng Hills, and that it formed the Solo terrace sequence between 316 and 31 ka and the Ngandong terrace between about 140 and 92 ka. Non-human fossils recovered during the re-excavation of Ngandong date to between 109 and 106 ka (uranium-series minimum) and 134 and 118 ka (US–ESR), with modelled ages of 117 to 108 thousand years (kyr) for the H. erectus bone bed, which accumulated during flood conditions These results negate the extreme ages that have been proposed for the site and solidify Ngandong as the last known occurrence of this long-lived species.

Yan Rizal, et al., "Last appearance of Homo erectus at Ngandong, Java, 117,000–108,000 years ago" Nature (December 18, 2019). doi:10.1038/s41586-019-1863-2

Reflections On Greece Part I: Palimpsest Layers In The History Of Greece

So, I am back from a couple of weeks in Greece, in Athens, the Cyclades, and Crete. Naturally, this got me thinking about a lot of issues of deep history. I'll start with a historical backgrounder.

The Eastern Mediterranean (image from here).

Any assessment of genetic or archaeological or linguistic evidence from Greece and historiography require one to consider the many confounding palimpsest layers in its past that must be considered and stripped away before considering older materials.

Greece had Neanderthals and the earliest modern humans in Europe (as expected almost definitionally as it is the most Southeastern part of Europe).

A One Paragraph Overview Of Holocene Era Greek History

Wikipedia sums up its history this way:

Generally, the history of Greece is divided into the following periods:

• Neolithic Greece covering a period beginning with the establishment of agricultural societies in 7000 BC and ending in 3200/3100 BC,
• Helladic (Minoan or Bronze Age) chronology covering a period beginning with the transition to a metal-based economy in 3200/3100 BC to the rise and fall of the Mycenaean Greek palaces spanning roughly five centuries (1600–1100 BC),
• Ancient Greece covering a period from the fall of the Mycenaean civilization in 1100 BC to 146 BC spanning multiple sub-periods including the Greek Dark Ages (or Iron Age, Homeric Age), Archaic period, the Classical period and the Hellenistic period,
• Roman Greece covering a period from the Roman conquest of Greece in 146 BC to 324 AD,
• Byzantine Greece covering a period from the establishment of the capital city of Byzantium, Constantinople, in 324 AD until the fall of Constantinople in 1453 AD,
• Ottoman Greece covering a period from 1453 up until the Greek Revolution of 1821,
• Modern Greece covering a period from 1821 to the present.

Greece was near the birthplace of the Fertile Crescent Neolithic and had very early Neolithic communities. 

Bronze Age Greece

Greeks metal age civilizations including the Minoan civilization were among the earliest, if not the earliest, in Europe, and were pre-Indo-European. A parallel, somewhat less advanced metal age culture arose on the Greek mainland.

Greece has one of the best documented transitions from the non-Indo-European to Indo-European cultures in prehistory with even some written attestation in the form of the Linear A to Linear B and Eteocretan transitions in addition to rich oral legendary history documented not too long after fact, and contemporaneous Akkadian and Egyptian records.

Iron Age And Early Medieval Greece

In the Iron Age, Greece had periods of Persian invasion and rule. Briefly, in the early Iron Age, before the Romans became ascendant, they had an ancient maritime colonial civilization that stretched from the Mediterranean coast in Spain to the Black Sea. Culturally and linguistically, "Ancient" and "Classical" Greece in the early Iron Age were in direct cultural continuity with the Mycenaean Greek society that fell during Bronze Age collapse.

The Roman Empire at its greatest extent, 117 CE, the time of Trajan's death (with its vassals in pink) via Wikipedia.

Fun fact: Emperor Hadrian, who is famous for his wall in Britain at something close to the Roman Empire's peak, also built an archway in new half of the city in Athens that survives today and is now at the center of the city. I checked it out in person the day before yesterday.

They spent four and a half centuries ruled by the Romans.

But, they are one of the best examples of a people who were conquered militarily but ended up culturally integrating and subsuming their conquerors to a great extent. When the Western Roman Empire collapsed, the Greek speaking Eastern Roman Empire survived and morphed into the Byzantine Empire centered in Constantinople, which prevailed in Greece for another eleven centuries (although this was not uniform across all parts of Greece).

Ottoman and Venetian Greece In The Late Middle Ages And Early Modern Period

The division of the Byzantine Empire after the Fourth Crusade (1204-1261 CE) via Wikipedia. The purple territory is the Byzantine Empire proper and the rust colored states are Greek successor states of the Byzantine Empire. The green areas are parts of the Republic of Venice shown with the year that they joined the Republic of Venice. The Brown Sultanate is an immediate predecessor of the Ottoman Empire which would come into being a generation later. 

The Byzantine Empire greatly reduced since the 7th century, in the face of an expanding Islamic Empire, lasted for eight centuries, but it was all downhill after 1261 CE, and finally imploded in 1453 CE, after being defeated by the Ottoman Empire (1299-1922 CE).

The Republic of Venice in the 15th and 16th centuries via Wikipedia.

The Ottoman Empire at its greatest extent in Europe, under Sultan Mehmed IV via Wikipedia.

But, some of Greece resisted the Islamic expansion by becoming an integral part of the Republic of Venice for many centuries with Heraklion, the current regional capital of Crete, becoming a Venice of the East (the understanding that the term "Oriental" originally referred to what is now often referred to as the "Near East" sunk in).

Eventually the Ottoman Empire did conquer Greece, but this left a remarkably thin lasting impression. Even the "Turkish delights" made famous by C.S. Lewis are called "Greek delights" everywhere in Greece which is allergic to Turkey with whom it has a tortured history of conflict that is ongoing. A brief period of Greek absolute monarchy under Austro-Hungarian King Otto's brother-in-law (from 1832 to 1843 when he established a constitutional monarchy in which he remained king) left more of a lasting mark on the country than about four centuries of Ottoman Empire rule.

A more detailed account of the process explains that:

Most of Greece gradually became part of the Ottoman Empire in the 15th century. The Eastern Roman, the direct continuation to the ancient Roman Empire who ruled most of the Greek-speaking world for over 1100 years, had been fatally weakened since the sacking of Constantinople by the Latin Crusaders in 1204. 

The Ottoman advance into Greece was preceded by a victory over the Serbs to its north. First, the Ottomans won at 1371 on the Maritsa River – where the Serb forces were led by the King Vukašin of Serbia, the father of Prince Marko and the co-ruler of the last emperor from the Serbian Nemanjic dynasty. This was followed by a draw in the 1389 Battle of Kosovo. 

With no further threat by the Serbs and the subsequent Byzantine civil wars, the Ottomans captured Constantinople in 1453 and advanced southwards into Greece, capturing Athens in 1458. The Greeks held out in the Peloponnese until 1460, and the Venetians and Genoese clung to some of the islands, but by 1500 most of the plains and islands of Greece were in Ottoman hands. The mountains of Greece were largely untouched, and were a refuge for Greeks to flee foreign rule and engage in guerrilla warfare. 

Cyprus fell in 1571, and the Venetians retained Crete until 1670. The Ionian Islands were only briefly ruled by the Ottomans (Kefalonia from 1479 to 1481 and from 1485 to 1500), and remained primarily under the rule of Venice. 

Territorial evolution of Kingdom of Greece until 1947 CE via Wikipedia. 
The territories in yellow, acquired in 1920, were ceded back to Turkey in 1923. 

Eventually, staring with the proclamation of the Greek Revolution in October of 1821, the Greeks finally secure independence after a long hiatus (I'm not sure that Greece was ever a unified kingdom before this time, as opposed to a civilization of interacting balkanized city-states and small principalities, even in its Golden Age). This was a period of tremendous growth, urbanization and modernization, a bit like that of countries emerging from Eastern Europe and the Communist regimes in the 20th century. As explained here:

The urban population tripled from 8% in 1853 to 24% in 1907. Athens grew from a village of 6000 people in 1834, when it became the capital, to 63,000 in 1879, 111,000 in 1896, and 167,000 in 1907.

In Athens and other cities, men arriving from rural areas set up workshops and stores, creating a middle class. They joined with bankers, professional men, university students, and military officers, to demand reform and modernization of the political and economic system. Athens became the center of the merchant marine, which quadrupled from 250,000 tons in 1875 to more than 1,000,000 tons in 1915. As the cities modernized, businessmen adopted the latest styles of Western European architecture.

This was actually the second rebirth of Athens, which was also entirely abandoned in favor of a more defensible neighboring island in the 400s BCE, following a Persian invasion. Athens is now home to about 4 million people, a third of the twelve million people in modern Greece, more than half of whom live in its three largest cities (only about 12% of the population lives permanently on its islands today, and most of those people live in urban settings as well).

With more than a century of territorial adjustments, Greece eventually reached something like its current boundaries. For example, as a result of the Balkan Wars of 1912–1913, most of Epirus, southern Macedonia, Crete and the northern Aegean islands were incorporated into the Kingdom of Greece. Greece was divided internally between the major sides in World War I with the prevailing allies ousting the King and becoming ascendant. Today's boundaries of Greece are the same as they were in 1919, except for the Dodecanese islands off the shore of Turkey ceded by Italy to Greece in 1947.

The 19th and 20th century brought major territorial realignments and mass migrations of people "ethnic cleansing" style with non-Greeks leaving independent Greece and Greeks with a handful of exceptions leaving Anatolia and the Black Sea region (something reminiscent of the mass migrations of Jews leading up to World War II and for those who survived the Holocaust, in its aftermath, to Israel and the United States, and also of the realignment of populations in South Asia following the partition of India and Pakistan).

Per Wikipedia, in the next key time period:

At the end of the war, the Great Powers agreed that the Ottoman city of Smyrna (Izmir) and its hinterland, both of which had large Greek populations, be handed over to Greece. 

Greek troops occupied Smyrna in 1919, and in 1920 the Treaty of Sèvres was signed by the Ottoman government; the treaty stipulated that in five years time a plebiscite would be held in Smyrna on whether the region would join Greece. However, Turkish nationalists, led by Mustafa Kemal Atatürk, overthrew the Ottoman government and organised a military campaign against the Greek troops, resulting in the Greco-Turkish War (1919-1922). A major Greek offensive ground to a halt in 1921, and by 1922 Greek troops were in retreat. The Turkish forces recaptured Smyrna on 9 September 1922, and setting the city ablaze and killing many Greeks and Armenians. 

The war was concluded by the Treaty of Lausanne (1923), according to which there was to be a population exchange between Greece and Turkey on the basis of religion. Over one million Orthodox Christians left Turkey in exchange for 400,000 Muslims from Greece. The events of 1919–1922 are regarded in Greece as a particularly calamitous period of history. Between 1914 and 1923, an estimated 750,000 to 900,000 Greeks died at the hands of the Ottoman Turks, in what many scholars have termed a genocide.

World War II was not kind to Greece either, where it was a major area of active conflict, and a period of Nazi occupation left definite marks. Once restored to allied control, civil war between nationalist and communist forces broke out (1944-1949) before World War II was even over, in the first conflict of the Cold War. Subsequent U.S. led post-war Marshall Plan reconstruction efforts that flooded Athens or other major Greece cities with "International style" "brutalist" architecture that remains predominant in much of the mainland. 

Neither the monarchy nor democratic nature of the constitutional monarchy was uninterrupted:

Following the National Schism during World War I and the subsequent Asia Minor Disaster, the monarchy was deposed in March 1924 and replaced by the Second Hellenic Republic. Between 1924 and 1935 there were in Greece twenty-three changes of government, a dictatorship, and thirteen coups d'etat. In October 1935, General Georgios Kondylis, a former Venizelist, overthrew the government and arranged for a plebiscite to end the republic. On 3 November 1935, the official tally showed that 98% of the votes supported the restoration of the monarchy. The balloting was not secret, and participation was compulsory. As Time described it at the time, "As a voter, one could drop into the ballot box a blue vote for George II and please General George Kondylis, or one could cast a red ballot for the Republic and get roughed up." George II returned to the Greek throne on 25 November 1935. 

On 4 August 1936, the King endorsed the establishment of a dictatorship led by veteran army officer Ioannis Metaxas, signing decrees that dissolved the parliament, banned political parties, abolished the constitution, and purported to create the "Third Hellenic Civilization." An Index of banned books during that period included the works of Plato.

George II followed the Greek government in exile after the German invasion of Greece in 1941 and returned to the throne in 1946, after a referendum that resulted in the restoration of constitutional monarchy.

Greece got yet another military coup and military dictatorship (which abolished the constitutional monarchy once and for all) in 1967 and lasted until 1974 when it fell to another coup that also precipitated a coup in Cyprus that led to the Turkish invasion of Cyprus whose consequences remain a point of tension that has not been fully resolved.

In 1967, the Greek military seized power in a coup d'état, overthrowing the centre right government of Panagiotis Kanellopoulos. It established the Greek military junta of 1967-1974 which became known as the Régime of the Colonels. The junta government's accession to power lead to an isolation to Greece from European affairs and froze Greece's entry to the European Union. In 1973, the régime abolished the Greek monarchy and in 1974, dictator Papadopoulos denied help to the United States. After a second coup that year, Colonel Ioannides was appointed as the new head-of-state. 

Ioannides was responsible for the 1974 coup against President Makarios of Cyprus. The coup became the pretext for the first wave of the Turkish invasion of Cyprus in 1974 (see Greco-Turkish relations). The Cyprus events and the outcry following a bloody suppression of Athens Polytechnic uprising in Athens led to the implosion of the military régime.

But, democracy was ended and the end of the monarchy was confirmed, later in 1974, and Greece joined the E.U.

After the end of the military régime, democracy was restored. 

The fall of the junta was followed by the metapolitefsi. Metapolitefsi was initiated when Konstantinos Karamanlis returned from self-exile in Paris at the invitation of the junta, to become interim prime minister on July 23, 1974 and later gained re-election for two further terms at the head of the conservative New Democracy Party. In August 1974, Greek forces withdrew from the integrated military structure of NATO in protest at the Turkish occupation of northern Cyprus. 

In 1974, a referendum voted 69%–31% to confirm the deposition of King Constantine II. A democratic republican constitution came into force. Another previously exiled politician, Andreas Papandreou also returned and founded the socialist PASOK Party (Panhellenic Socialist Movement), which won the 1981 election and dominated Greek politics for almost two decades. 

After the restoration of democracy, Greece's stability and economic prosperity improved significantly. Greece rejoined NATO in 1980, joined the European Union (EU) in 1981 and adopted the euro as its currency in 2001.

This didn't bring happily ever after, however. 

In 2009, a sovereign debt crisis flowing from a U.S. led global financial crisis hit Greece and the country was thrust into a state of extreme economic distress until about 2015. Everywhere in Greece there are abandoned half built homes and commercial buildings, the construction of which was derailed in that crisis, which have not completed and are covered with graffiti, some serving as homeless camps, as of August of 2019. Successive elections brought tidal waves of political change and also gave far right parties considerable power, although the far right parties and more democratic socialist leaning parties were swept out earlier this year in an election that brought a center-right party into power, and as I my visit, affairs had returned to relative normalcy. 

Beliefs About Bees In The Balkans

Slavs believed that bees were the purest beings and the only ones whose soul devil can't corrupt and that beehives are the only place where devil can't hide.... In South Slavic languages, the word "uginuti" means "to die" but is only used for animals. The word "umreti" also means "to die" but is only used for people. And bees... The reason for this could be that in some parts of Serbia people believed that the soul of the deceased migrated into a bee. So bees and humans had the same soul. Slavs believed that bee only bites people who committed some kind of sin. In Lika (Croatia), at Christmas people would fill a small wooden vessel used for scooping flour from storage with grains, and would stick three beeswax candles in the grain, one for dead, one for bees and one for grain.

From the Old European Culture blog.

There are also rituals which strongly suggest that the ancient Slavs knew that bees were closely linked to the fertility of grain, although they probably did not know precisely the way that pollination caused this to occur.

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.

Andean Elevation Adaptations Differ From Tibetan Ones

In Tibet, human hypoxia response was a major evolutionary adaptation to high elevations (probably acquired via introgression from archaic hominins called Denisovans). In the Andean highlands, in contrast, where the potato was domesticated, there are adaptations for starch digestion but not for hypoxia.

The Andean highland people also demonstrate the widely recognized reality that highlands and other inaccessible places tend to be refugia for populations wiped out elsewhere, while lowlands are more vulnerable to population replacement.

The genetic split date between low and high elevation populations in the Andean mountains, however, ca. 7150 BCE to 6150 BCE, is surprisingly recent for a territory that modern humans had very likely colonized by 12000 BCE.

The peopling of the Andean highlands above 2500m in elevation was a complex process that included cultural, biological and genetic adaptations. Here we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7,000 calendar years before present (BP), and compare them to 64 new genome-wide genetic variation datasets from both high and lowland populations. 

We infer three significant features: a split between low and high elevation populations that occurred between 9200-8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. 

Importantly, we do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.

John Lindo, et al., "The genetic prehistory of the Andean highlands 7,000 Years BP though European contact" bioRxiv (July 31, 2018). 

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Sparrows Co-Evolved With Human Agriculture To Digest Grains More Efficiently

In an ideal world, more papers on subjects like the emergence of agriculture would incorporate corroborating data points like this one that make the narrative robust and more rich.

House sparrows (Passer domesticus) are a hugely successful anthrodependent species; occurring on nearly every continent. Yet, despite their ubiquity and familiarity to humans, surprisingly little is known about their origins. We sought to investigate the evolutionary history of the house sparrow and identify the processes involved in its transition to a human-commensal niche. 

We used a whole genome resequencing dataset of 120 individuals from three Eurasian species, including three populations of Bactrianus sparrows, a non-commensal, divergent house sparrow lineage occurring in the Near East. 

Coalescent modelling supports a split between house and Bactrianus sparrow 11 Kya and an expansion in the house sparrow at 6 Kya, consistent with the spread of agriculture following the Neolithic revolution. Commensal house sparrows therefore likely moved into Europe with the spread of agriculture following this period. Using the Bactrianus sparrow as a proxy for a pre-commensal, ancestral house population, we performed a comparative genome scan to identify genes potentially involved with adaptation to an anthropogenic niche. We identified potential signatures of recent, positive selection in the genome of the commensal house sparrow that are absent in Bactrianus populations. The strongest selected region encompasses two major candidate genes; COL11A—which regulates craniofacial and skull development and AMY2A, part of the amylase gene family which has previously been linked to adaptation to high-starch diets in humans and dogs. Our work examines human-commensalism in an evolutionary framework, identifies genomic regions likely involved in rapid adaptation to this new niche and ties the evolution of this species to the development of modern human civilization.

Mark Ravinet,, et al., "Signatures of human-commensalism in the house sparrow genome" Proceedings of the Royal Society B (August 8, 2018) via this tweet (hat tip Razib Khan).

The Ecology Of An Empire

There are many apocryphal quotes attributed to Genghis Khan. And there’s a reason for that — in a single generation he led an obscure group of Mongolian tribes to conquer most of the known world. His armies, and those of his descendants, ravaged lands as distant as Hungary, Iran and China. After the great wars, though, came great peace — the Pax Mongolica. But the scale of death and destruction were such that in the wake of the Mongol conquests great forests grew back from previously cultivated land, changing the very ecosystem of the planet.

From here.

How Did One Language Family Come To Dominate Australia Prior To European Contact?

It remains a mystery how Pama–Nyungan, the world’s largest hunter-gatherer language family, came to dominate the Australian continent. Some argue that social or technological advantages allowed rapid language replacement from the Gulf Plains region during the mid-Holocene. Others have proposed expansions from refugia linked to climatic changes after the last ice age or, more controversially, during the initial colonization of Australia. Here, we combine basic vocabulary data from 306 Pama–Nyungan languages with Bayesian phylogeographic methods to explicitly model the expansion of the family across Australia and test between these origin scenarios. We find strong and robust support for a Pama–Nyungan origin in the Gulf Plains region during the mid-Holocene, implying rapid replacement of non-Pama–Nyungan languages. Concomitant changes in the archaeological record, together with a lack of strong genetic evidence for Holocene population expansion, suggests that Pama–Nyungan languages were carried as part of an expanding package of cultural innovations that probably facilitated the absorption and assimilation of existing hunter-gatherer groups.

Remco R. Bouckaert, Claire Bowern & Quentin D. Atkinson "The origin and expansion of Pama–Nyungan languages across Australia" Nature Ecology & Evolution (March 12, 2018).

Skepticism is in order because New Zealander Quentin D. Atkinson has a history of relying on math that fails to honor existing linguistic knowledge resulting in clearly wrong predictions. But, his hypothesis here is, at least, strongly conventional wisdom confirming.

My strong suspicion is that the key cultural innovation was the integration of the Dingo into Australian society after ca. 50,000-60,000 previous years without dogs. The epicenter of this expansion coincides perfectly with the expected location of an introduction of the Dingo into Australia, and the Dingo is also known to have resulted in a second wave of mass extinctions of local fauna in Australia.

Savannah Ecologies Of Africa, India and Eurasia Were Once Connected

The scene was set for hominin evolution on the savannah in Africa in the late Miocene era, a geological epoch that spans from 23,030,000 to 5,333,000 years ago. 

Despite much interest in the ecology and origins of the extensive grassland ecosystems of the modern world, the biogeographic relationships of savannah palaeobiomes of Africa, India and mainland Eurasia have remained unclear. Here we assemble the most recent data from the Neogene mammal fossil record in order to map the biogeographic development of Old World mammalian faunas in relation to palaeoenvironmental conditions. Using genus-level faunal similarity and mean ordinated hypsodonty in combination with palaeoclimate modelling, we show that savannah faunas developed as a spatially and temporally connected entity that we term the Old World savannah palaeobiome. The Old World savannah palaeobiome flourished under the influence of middle and late Miocene global cooling and aridification, which resulted in the spread of open habitats across vast continental areas. This extensive biome fragmented into Eurasian and African branches due to increased aridification in North Africa and Arabia during the late Miocene. Its Eurasian branches had mostly disappeared by the end of the Miocene, but the African branch survived and eventually contributed to the development of Plio–Pleistocene African savannah faunas, including their early hominins. The modern African savannah fauna is thus a continuation of the extensive Old World savannah palaeobiome.

Ferhat Kaya, et al., "The rise and fall of the Old World savannah fauna and the origins of the African savannah biome" Nature Ecology and Evolution (January 1, 2018).

Papuans Continued To Forage Long After Inventing Agriculture

In most places where agriculture was adopted, it replaced hunting and foraging. But, new hard evidence based upon isotypes in small mammal bones in Papua New Guinea demonstrates that there, foraging remained an important source of subsistence until at least 300 years ago. As a Science Daily press release explains:

In tropical New Guinea, where one of the earliest human experiments with agriculture occurred, agriculture apparently never replaced foraging as a primary subsistence strategy: "Montane tropical forest environments provided a stable source of subsistence for human hunter-gatherers in New Guinea," says Patrick Roberts, primary author of the study. "We have found out that foragers were living in close proximity to emerging farming groups, from 12,000 to 300 years ago, which indicates that agriculture was not a forced event in this part of the world." 

Tropical forests have frequently been perceived as unattractive habitats for humans -- both foragers and farmers -- due to poor soils, difficulties of humidity, and issues of reliable nutrition. However, archaeological work in New Guinea, among other tropical regions, has now helped to refute this idea: "We can now affirm that humans have occupied areas in this region, covered today in rainforest, from 45,000 years ago," says..., Professor Glenn Summerhayes from the University of Otago, senior author of the study. "Some of the earliest evidence for the human development of agriculture comes precisely from the tropical forested portions of New Guinea."

This is particularly notable, because most cultures in global history that have been slow adopters of agriculture have had a predominantly fishing based economy as an alternative, but in New Guinea we have a group of terrestrial hunter-gatherers in a tropical forest instead.

The abstract and citation to the source article are as follows:

The terminal Pleistocene/Holocene boundary (approximately 12–8 thousand years ago) represented a major ecological threshold for humans, both as a significant climate transition and due to the emergence of agriculture around this time. In the highlands of New Guinea, climatic and environmental changes across this period have been highlighted as potential drivers of one of the earliest domestication processes in the world. We present a terminal Pleistocene/Holocene palaeoenvironmental record (12–0 thousand years ago ) of carbon and oxygen isotopes in small mammal tooth enamel from the site of Kiowa. The results show that tropical highland forest and open mosaics, and the human subsistence focused on these environments, remained stable throughout the period in which agriculture emerged at nearby Kuk Swamp. This suggests the persistence of tropical forest foraging among highland New Guinea groups and highlights that agriculture in the region was not adopted as a unilinear or dramatic, forced event but was locally and historically contingent.

Patrick Roberts, Dylan Gaffney, Julia Lee-Thorp, and Glenn Summerhayes. "Persistent tropical foraging in the highlands of terminal Pleistocene/Holocene New Guinea." 1 Nature Ecology & Evolution 44 (2017).