ancient DNA

A ‘Mysterious’ New Frog Species With Hidden Spots and an Insect-Like Call

Discovered in the Western Ghats of southern India, the species is unique enough to be placed in a newly-created genus as well.

It was after a heavy spell of rain during the 2015 monsoon that Sonali Garg walked out to a spot she had been visiting regularly, and unsuccessfully, for more than two years. A large muddy puddle.

But this time, she struck gold in the form of a new species of frog, Mysticellus franki sp. nov., which turned out to be so unique the study authors have assigned it to a newly created genus.

It all started in 2013 when Garg encountered “strange looking” tadpoles in that muddy puddle when conducting amphibian surveys for her PhD from Delhi University. It was clear the tadpoles belonged to the frog family Microhylidae, but beyond that, “we couldn’t pinpoint what species the tadpoles belonged to,” said Garg in an interview with Mongabay.

When the researchers sequenced the tadpoles and examined the DNA, it was clear that the tadpoles were of a hitherto unknown frog species.

“We have a library of sequences of frogs and other amphibians from the country and we could compare the sequence of the unknown tadpole against them,” said Garg. “To our surprise, the sequence did not match any frog species from the country; it fell into the family [Microhylidae], but beyond that, it did not match anything that was known from India.”

With no knowledge about the adult frog — where it was found, whether it was big or small. Garg and her team started visiting the puddle where they collected the tadpoles regularly. An adult specimen was needed to carry out the necessary morphological analyses to delve into the mysterious new species.

“For the next two years, we kept going back to the same spot. It was the only spot we were sure we would get it,” said Garg. “So we went back there at different seasons and different times of the year because we didn’t know when this frog would come out.”

“Eventually, after two years of this exercise of repeated searching, one monsoon, a couple of days after the monsoon hit, when there was sufficient water that collected on the ground, around the puddles … we saw the frogs. They were there in the hundreds, it was magical. It was as if the frogs were welcoming us,” she added, the excitement still palpable in her voice even after nearly four years.

The new species “was an accidental discovery,” said Garg and supervisor S.D. Biju. “We just happened to be at the right place, at the right time. And of course, often we fail to look closely. In this case, we looked closely at every tadpole, and that’s how this discovery happened!”

Male and female specimens of the newly discovered Mysticellus franki sp. Credit: S.D. Biju

A new species … and a new genus

After making careful notes from the field and recording the calls of the male frogs serenading for females in the puddles, the researchers collected specimens and brought them to the lab to carry out genetic analyses.

A combination of genetic, morphological and call data threw up the final diagnosis. The frog was definitely a new species, and sufficiently different from other members of the family Microhylidae found in India to be assigned to its own genus as well.

The new species belongs to sub family Microhylinae. The genus name Mysticellus is derived from the Latin mysticus, meaning mysterious, and ellus, which means diminutive. The name highlights “the ability of this small frog to remain out of sight despite its occurrence in wayside areas surrounding human settlements,” write the authors in the paper. The species name franki honours Franky Bossyut, a professor and amphibian biologist at Vrije Universiteit Brussel.

“I agree with assignment of the species status. The allocation of a genus status is motivated based on molecular evidence. The evidence is still tenuous because we have one member of the new genus,” said Karthikeyan Vasudevan, senior principal scientist at the Laboratory for the Conservation of Endangered Species (LACONES), Centre for Cellular and Molecular Biology.

“More than anything, it is surprising that it has not been already found and described. While very similar in shape, size, and colouration to other microhylid frogs in southeast Asia, there is nothing in the Western Ghats of India that resembles this,” said David Blackburn, the Associate Curator of Amphibians and Reptiles at the Florida Museum of Natural History. “It is only the secretive nature of these frogs that has resulted in them only now being known to science.”

The new species of frog was discovered when researchers came across a ‘strange’ looking tadpole. After continuously searching for an adult for two years, they spotted around 100 adult frogs around a roadside puddle. Credit: S.D. Biju

Hidden spots and an insect-like call

The researchers observed that the frogs started congregating in hundreds around temporary muddy puddles, two to three days after the first monsoon showers. After four to five days of intense breeding, the frogs disappeared completely, leaving the researchers mystified.

“After we first discovered this frog in 2015, we carried out several surveys in and around the region over a period of three years to study this frog. However, due to its secretive behaviour we were only able to locate it during a very short window of less than four days,” said the authors in an interview.

After the frogs disappeared, the researchers were not able to locate “even a single individual” at any other time of the year. “We don’t know where it hides, lives, and what it does for the rest of the year. The frog’s external appearance does not show morphological adaptations for burrowing. At the same time, we doubt that it simply hides under leaf litter, rocks and stone (the usual hiding places for frogs during the non-breeding time). It’s still a mystery for us,” they said.

When the males called to attract females, they raised the hind part of the body to show off “a pair of black false-eye like spots.” The frogs did the same when the researchers tried to approach them, said Garg.

“The effect is quite startling,” she said. “When the animal is sitting down, the spots are hidden. When we were close to the animal, the frog raised the hind part of its body. This movement really made the spots very visible.”

“The best guess we have is that it’s a defensive mechanism,” she said.

The call of the frog is also quite distinct, observed the researchers. “It resembles an insect chorus,” write the authors in the press release.

The frogs probably had such a unique call to attract females in the most efficient manner, said Garg. “Even if a puddle is crowded with multiple frog species and multiple individuals of the same species, even if it’s pitch dark, the female needs to be able to find her way to the male,” she said. “This is one reason to have unique calls. Also, for this species, with such a short breeding window of four or five days, the pressure to get it right is much higher,” she added.

The frog has two distinct eye-like spots on its rear-end which probably serve as a self-defence feature. Credit: S.D. Biju

A mysterious past

A phylogeny (a sort of family tree) of all known genetic data known from the family Microhylidae shows that the closest relative of the subfamily Microhylinae is the subfamily Dyscophinae, which is restricted to Madagascar.

The available molecular evidence gives us this story. The family Microhylidae would have originated on Gondwanaland, the ancient supercontinent which would eventually break up to form most of South America, Africa, the Indian subcontinent, Australia and Antarctica. When Gondwanaland broke up, the subfamily Dyscophinae took up home in Madagascar and sub family Microhylinae moved on toward Asia on the Indian subcontinent. The split between Dyscophinae and Microhylinae happened about 67 million years ago, giving Microhylinae enough time to diversify in the Indian subcontinent as it drifted along towards Eurasia. Once the Indian subcontinent docked at Eurasia, frogs that make up the Microhylinae subfamily spread all over Asia.

For M. franki in particular, the closest relative on the family tree is the genus Micryletta, also belonging to subfamily Microhylinae but found in the Indo-Burma and Sunderland biodiversity hotspots in Southeast Asia and China.

Using algorithms that can parse out evolutionary timelines by considering the rate at which DNA changes over time, the researchers were able to give tentative dates to different nodes of the phylogeny.

The secretive frogs vanished after appearing for the breeding season which lasted for around four days. Credit: S.D. Biju

“Our study shows that the common ancestors of Mysticellus and Micryletta diverged about 40 million ago. Most likely they originally inhabited the Indian Peninsula and later diverged to give rise to both these genera,” said the authors.
The authors posit that the two genera are likely to have split when the Indian landmass moved close to mainland Southeast Asia through the Myanmar-Malay Peninsula during Middle/Late Eocene.

Karthikeyan Vasudevan from LACONES said, “Recent evidence from the study of arthropods in amber suggests that prior to the final collision at around 55 million years ago with Asia, India moved close to or had land connections with Africa and Europe.” Some models of continental drift show that species could have moved between the Indian subcontinent and Southeast Asia prior to the former’s collision with Asia, he added.

“This might help explain the presence of genera that are not present in the Eastern Himalayas, but are found in South India, Sri Lanka and Southeast Asia,” he added. He gave examples of the skink genus Dasia and the pit vipers (genus Tropidolaemus).

David Blackburn from the Florida Museum of Natural History agrees. “Clearly, some lineages must have survived on India as it moved across the Indian Ocean during the late Mesozoic and early Cenozoic, but several studies, including this one, now support that colonisation of the Indian subcontinent by animals from Asia before India had fully collided with the Asian mainland,” he said.

With inputs from Sahana Ghosh.

This article was first published on Mongabay. Read the original here.

Ancient Teenager the First Known Person with Parents of Two Different Species

Ancient DNA in a 50,000+ year old bone tells us that two species of early humans did produce offspring together. But how did a Neanderthal woman meet a Denisovan man? How did their respective communities interact? These are questions that now must be asked and investigated.

A new ancient DNA study published in Nature today reports the first known person to have had parents of two different species. The studied remains belonged to a girl who had a Neanderthal mother and a Denisovan father.

Neanderthals (Homo neanderthalensis) lived throughout Europe and Western Asia until around 30,000 years ago. This species lived in several different ecological zones, survived three glacial periods, and were excellent hunters and tool-makers.

Denisovans (Homo sapiens denisova), on the other hand, we know very little about. Thus far they have only been found in Denisova Cave in Sibera as tiny bone fragments. We don’t yet know what they looked like – nor exactly what they were capable of.

Neanderthal, Denisovans, and modern humans all shared a common ancestor more than 400,000 years ago.

Is this what Denisova 11’s mother looked like? A museum model of a Neanderthal woman. Credit: Shutterstock

Found in Denisova Cave, this child – known as “Denisova 11” – was at least 13 years of age at the time of her death. Analysis of a piece of her bone found that the girl died more than 50,000 years ago.

This discovery occurred through ancient DNA analysis, whereby a small piece of the teenager’s bone was pulverised, the DNA extracted, and then sequenced. The sequence was then compared to previously analysed samples from Neanderthals, modern humans, and Denisovans. Her genetic traits could only be explained if her mother was a Neanderthal and her father was a Denisovan.

Denisova 11 was a first generation Neanderthal-Denisovan woman – perhaps we could call her a “Neandersovan”?

Over many thousands of years, Denisova Cave in Siberia was occupied by Denisovans, Neanderthals and modern humans. Credit: Google Earth

Neighbours of modern humans

Neanderthals and Denisovans inhabited Eurasia until about 40,000 years ago when they were replaced by modern humans (Homo sapiens).

But before this replacement occurred, there appears to have been a fair bit of mingling going on whenever the different groups met.

Indeed, the ancestors of modern-day Oceanians and Asians contain Denisovan DNA, while present-day non-Africans contain 2-4% Neanderthal DNA.

Where ancient people roamed: the valley above the Denisova Cave archaeological site, Russia. Credit: Bence Viola

More mobile than we thought

The DNA of this girl — Denisova 11 — also suggests that there was some quite significant movement of Neanderthal groups between Western Europe and the East. Analysis of her DNA found that rather than being more closely related to a Neanderthal who lived in her home cave sometime prior to her birth, she instead showed more connections to those recovered in Western Europe.

This finding is interesting because most archaeological evidence indicates that Neanderthals – unlike modern humans – were not interested in long-distance movement. They don’t seem to have moved much beyond relatively constrained territories which provided everything they needed for day-to-day life.

Denisova 11 suggests that at least some major movement of ancient humans occurred between west and east. But when? And why?

And how did a Neanderthal woman meet a Denisovan man? How did their respective communities interact? These are questions that now must be asked and investigated.

Mystery girl

While this young girl has told us so much about her ancestors, we know very little about her.

Because it was only a small piece of one of her long bones found, we don’t know how she died. We can’t know if she suffered any serious illness in her short life, nor if she ever broke a bone.

We only know that she lived.

Michelle Langley, ARC DECRA Research Fellow, Griffith University

This article was originally published on The Conversation. Read the original article.

What a 2,000-Year-Old Skeleton Tells Us About a Mysterious Shipwreck

An ancient but shockingly advanced device called the Antikythera mechanism found among a shipwreck’s ruins left historians bamboozled for decades.

Divers investigate the shipwreck where the Antikythera mechanism was found. Source: Nature/YouTube

On August 31, marine archaeologist Brendan Foley’s diving team made a spine-tingling discovery in the bottom of the Aegean Sea: a human skeleton. The remains were part of a famous, ancient shipwreck estimated to have occurred sometime in the first century BC. And earlier this week, an ancient-DNA expert brought in by Foley confirmed that the bones had been preserved well enough to offer scientists, for the first time, a realistic chance finding a 2,000-year-old shipwreck victim’s DNA sample. As Jo Marchant reports in Nature News, such an analysis can potentially fill many gaps in our minimal knowledge about population movements in that era.

In 1900, Greek sponge divers first stumbled upon the shipwreck off the island of Antikythera. They alerted the government and the navy, who spent the next couple years salvaging artefacts from the site. Besides bronze statues, marble sculptures and showy pieces of glasswork, they also unearthed what is today considered to be the world’s first “analogue computer”. The level of complexity of this device with its gears, dials and wheels was shocking to historians because it did not seem to fit in with our imagining of those times.

Front view of the Antikythera mechanism. Credit: Marsyas/Wikimedia Commons, CC BY-SA 3.0

Later, it emerged that the Antikythera mechanism – as it was called – was used to show the lunar phases and the positions of the sun, moon and planets on any given date. The enigma surrounding this device highlighted to historians and scientists that the Antikythera shipwreck could serve as a window to a past we wrongly think we know a lot about.

However, the next large scale investigation into the site occurred only in 1976. This time, too, it did not disappoint. The French explorer Jacques-Yves Cousteau discovered hundreds more artefacts – coins, jars, jewellery, hull planks and, for the first time, human remains. These helped answer a few more questions about the wreck. The inscriptions on the coins and radiocarbon dating of the planks confirmed that the ship met with an accident sometime in the first century BC. The vessel was probably a merchant’s, inferred scientists, carrying luxury items from the eastern Mediterranean to be sold to rich Romans.

The next expedition began in 2012, when Foley began conducting a series of dives around the island. Improvements in diving technology allowed a deeper and hence more complete survey of the area. Over the next few years, according to Marchant, who has been tracking research on the shipwreck since the 2000s, the team accomplished robotic mapping surveys and discovered more luxury items among the ruins. Most notably, this June they found the first example of an ancient weapon, described in ancient texts as the ‘war dolphin’.

However, the big break was yet to come for Foley. On August 31, the underwater investigators found a set of bones, buried under sand and shards of pottery, all evidently belonging to the same individual. This person was presumed to have been a victim of the shipwreck. Judging from the bone’s quality, the scientists guess that it was a young male crew member, though this is yet to be confirmed. Although Cousteau had already found human remains in the 1970s, the recent find is more significant because the bones were found to be in remarkable condition, considering the circumstances.

Moreover, among the pieces of skull found, the petrous bones were found to be intact. Petrous bones are located behind the ear at the base of the skull. To ancient-DNA experts like Hannes Schroeder from Denmark, whom Foley invited to examine the remains, petrous bones are of special interest. Being one of the densest bones in the body, they are known for being one of the best sources of DNA, especially when the sample is found in non-frigid climes.

All Schroeder needs to proceed with DNA extraction is an OK from Greek authorities. If DNA is found, sequencing and analysis will be done, the results of which will be very exciting. “Human remains have started to become a source of information that can tell us incredible things about the past. Even with a single individual, it gives us a potentially great insight into the crew. Where did they come from? Who were these people?” Schroeder told The Guardian.

Ancient DNA analysis is not new to us. In 2010, the complete genome of a man who lived in Greenland 4,000 years ago was sequenced from a sample of his hair. The analysis of the genome showed that there was a migration from Siberia to Greenland more than 5,500 years ago. Based on the sequence, scientists were also able to reconstruct his appearance and predict his hair colour. In March this year, a small portion of the DNA from 430,000-year-old bones found in the mountains of Spain were successfully sequenced. The results added insight to our knowledge of human evolution, particularly when modern humans diverged from the Neanderthals.

Finding DNA in the Antikythera bones will be extra-special because these bones have not been treated with preservatives or been in contact with for a long time. This means the risk of contamination is relatively less. An analysis could reveal physical characteristics of the victim, allowing experts to deduce which part of the world he, and thus the ship, might have come from. It will allow us a more reliable glimpse into the civilisation that was apparently technologically advanced enough to have developed the world’s first computer, so to speak.