Humans

A human X (left) and Y chromosome seen with a scanning electron microscopeBIOPHOTO ASSOCIATES/Science Photo Library
Twenty years after the Human Genome Project was declared complete, the Y chromosome has been fully sequenced for the first time.
Most people have 22 pairs of chromosomes plus two sex chromosomes – either a pair of X chromosomes or one X and one Y chromosome. Having a Y usually – but not always – results in an embryo developing male characteristics.
The Y is one of the smallest chromosomes and has the fewest genes coding for proteins. Because it normally has no paired chromosome to swap pieces with prior to sexual reproduction, it is especially likely to accumulate bits of repetitive DNA.Advertisement
All early methods of DNA sequencing involved breaking DNA up into small pieces, reading their genetic code and then reassembling the pieces by looking for overlaps. This technique doesn’t work with repetitive DNA where lots of the pieces are identical.
Because of this, the “completed” human reference genome announced in 2003 was actually far from complete. “The Y chromosome just kept being pushed aside,” says Charles Lee at the Jackson Laboratory for Genomic Medicine in Connecticut. “It’s a hard chromosome to complete because of all the repetitive sequences.”
Only in 2021 did a team including Karen Miga at the University of California, Santa Cruz, finally fill in almost all the gaps, and again declare the human genome complete.
What made this possible is a technique, developed by a company called Oxford Nanopore, that reads the sequence of a single DNA molecule as it goes through a tiny hole, producing pieces that are millions of DNA letters long rather than a few hundred.
But the “complete” genome sequenced by Miga and her colleagues was a female one, consisting of the 22 normal chromosomes and the X chromosome. Only now have Miga’s team completed the Y chromosome as well, from a person of European descent.
“The Y chromosome is riddled with complicated structures and includes huge areas where the same blocks of code repeat over and over with minor variations, making its assembly quite challenging,” says Sergey Nurk, who worked on the project before getting a job at Oxford Nanopore. “[The] ability to sequence any-length fragments of DNA was absolutely instrumental for this project.”

This complete Y chromosome has 106 protein-coding genes, which is 41 more than in the reference genome. But almost all these extra genes are just copies of one gene called TSPY.
At the same time, Lee’s team has sequenced the Y chromosomes of 43 diverse men, including 21 of African origin. The teams were independent but did collaborate, says Lee.
However, only three of his team’s Y sequences are gapless, he says. The rest still have between one and five gaps.
The 43 Y chromosomes show considerable diversity, says Lee. For instance, the number of copies of the TSPY gene ranges between 23 and 39.
Whether the repetitive DNA in the Y does anything important remains unclear. “I believe there’s a lot to learn about repetitive DNA and we just don’t understand it yet, and so we’ve still dismissed it as junk,” says Lee.
But most biologists and clinicians have little interest in the repetitive DNA, says David Page at the Massachusetts Institute of Technology, who studies the Y chromosome. The sequencing has also revealed very little that is new about the “euchromatic” parts of the Y that do include genes, he says.
“The present study [by Miga’s team] represents an incremental advance in our understanding of the euchromatic portions, which were nearly complete 20 years ago,” says Page.

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Foundation season 2 is now out on Apple TV+Apple TV+
Struggling to choose what to watch? Whether it’s sci-fi, medical dramas or documentaries about the natural world, we have you covered on the CultureLab podcast. New Scientist‘s TV columnist Bethan Ackerley shares a rundown of her top TV choices from 2023 so far, as well as what to look out for the rest of the year. 

Transcript to follow.Advertisement
Reviews of some of the shows featured in this episode:  
Foundation (Apple TV+)
The Last Of Us (HBO Max and Sky Atlantic)
Best Interests (Sky Go, Amazon, Apple TV+)
Wild Isles (BBC iPlayer, Amazon)
Dead Ringers (Amazon)
Silo (Apple TV+)
To read all of Bethan’s TV columns visit newscientist.com/author/bethan-ackerley

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The mummified body of Ötzi, who is thought to have lived between 3350 and 3120 BC© South Tyrol Museum of Archaeology/Eurac/Marco Samadelli-Gregor Staschitz
A new genetic analysis has changed our understanding of Ötzi, the mummified “Iceman” who lived 5300 years ago and was found in a glacier in the Alps.
The findings reveal that almost all of Ötzi’s DNA was inherited from early farmers, who moved into Europe a few thousand years before he was born.
The genome also indicates that he had darker skin than any people with predominantly European ancestry today, and may well have … More

Academic, broadcaster and author Alice Roberts has just published her first children’s novel, Wolf Road. Set during the ice age 30,000 years ago, it follows the story of Tuuli, a prehistoric girl on a journey to her tribe’s summer camp who meets a strange boy on the way.
As this is Alice’s first children’s novel, New Scientist decided that the best person to quiz her about it was culture editor Alison Flood’s 10-year-old daughter Jenny, a big reader. Jenny asked Alice all the most important questions, including if people would really have made pets of wolf cubs, how Alice knows what life was like for people 30,000 years ago, and if she would rather live then or now.
Alice Roberts will be speaking at New Scientist Live in October. Tickets on sale now.

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Alice Roberts has a lot on her plate: she is a biological anthropologist, an author and a broadcaster, as well as professor of public engagement in science at the University of Birmingham, UK. But she has also found time to write her first children’s book, Wolf Road. Set during the ice age 30,000 years ago, it follows the story of Tuuli, a prehistoric girl on a journey to her tribe’s summer camp who meets a strange boy on the way.
Roberts joins New Scientist culture editor Alison Flood to talk about how she found writing fiction, the research she did for the novel and why she thinks it is important for children to know more about their past. “I wanted to write about the ice age,” she says. “I wanted to immerse people in that kind of ancient environment, in that ancient time, and use archaeology to build a world that then a story could unfold in.”
Alice Roberts will be speaking at New Scientist Live in October. Tickets on sale now.

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Aerial view of the excavation site in Jerusalem, at the foot of the Temple MountYair Izbotski/City of David
Archaeologists have reconstructed how Babylonian invaders burned down a building in Jerusalem more than 2500 years ago, using chemical clues in the debris.
The building was destroyed as part of the Babylonian conquest of the Kingdom of Judah, which is presented as a turning point in the story of Judaism in the Hebrew Bible.
Beginning in 601 BC, Judean kings launched a series of unsuccessful rebellions against the Babylonians, who had taken control of the region … More

The ancestor of Indo-European languages may have been spoken by farmers in southern Turkey 8000 years agoOdyssey-Images / Alamy Stock Photo
The common ancestor of Indo-European languages, which are now spoken by close to half the world’s population, was spoken in the eastern Mediterranean around 8000 years ago, according to an analysis of related words.
Indo-European languages, spanning from English to Sanskrit, have long been thought to share a common ancestor. The first linguist to make this link, William Jones, said in a lecture in 1786 that no linguist could examine Greek, Latin and Sanskrit together “without believing them to have sprung” from some common ancestor.
But researchers have struggled to agree on the origin story of this so-called proto-Indo-European language, says Paul Heggarty, who is now at the Pontifical Catholic University of Peru. There are two main hypotheses, he says.Advertisement
The first suggests that the language originated in the steppe region, north of the Black Sea, no earlier than 6500 years ago and then spread across Europe and parts of Asia with the domestication of horses.
The second, known as the farming theory, argues that the language was spoken far earlier and originated in the north of the Fertile Crescent, in what is now south-east Turkey and north-west Iran, as early as 9500 years ago and spread to other regions with the rise of farming.
To test these hypotheses, Heggarty and his colleagues created a database consisting of 170 words, such as “night” and “fire”, and their translations in 161 Indo-European languages, including 52 non-modern languages, such as ancient Greek.
By analysing shared patterns between the words, the researchers could estimate how related the languages were to each other and try to piece together when one language split into two new languages. “Languages don’t really have a date of birth, but you can see where there’s a split,” says Heggarty. “English is related to German, but these lineages separated from each other around 2000 years ago.”
Using this analysis, the team estimates that the root of all Indo-European languages dates back to around 8100 years ago. There is a good chance it originated in the Fertile Crescent as hypothesised by the farming theory, the researchers report. But while the farming theory suggests a close link between Indo-Iranic languages, such as Hindi, and Balto-Slavic languages, such as Latvian, the study found no clear evidence for this.
Instead, the researchers theorise that Indo-European languages spread in multiple directions from the Fertile Crescent. “One of those directions took it to the steppe, and from there, there was a secondary expansion to Europe,” says Heggarty.

They think this European expansion would have happened about 5000 years ago, as proposed by the steppe hypothesis. It is backed up by ancient DNA data that suggests there was a massive migration into Europe from the steppe region around that time. The team suggests that the Indo-Iranic branch of the language broke off earlier, around 7000 years ago.
This new “hybrid” idea therefore takes aspects of both the steppe and farming hypotheses. “This is the best framework to be working with now, as more research is coming in, especially from ancient DNA,” says Heggarty.
James Clackson at the University of Cambridge says this study is unlikely to be the final word on the origin of the Indo-European language family, but says it is a step in the right direction. “The creation of the open access database [of word meanings] is particularly welcome and I’m very grateful to the authors,” he says.

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Spices were traded between south Asia and South-East Asia more than 3000 years agoPeter Schickert/Westend61/Gett​y Images
People may have been cooking curries in South-East Asia for at least 2000 years, according to traces of spices found on freshly unearthed stone tools in Vietnam.
During their digs at the Oc Eo archaeological site in southern Vietnam, Hsiao-chun Hung at the Australian National University in Canberra and her colleagues uncovered several sandstone grinding tools alongside remnants of spices.
An analysis of 717 grains of starch recovered from the tools revealed eight types of spices: turmeric, ginger, galangal, sand ginger, fingerroot, clove, nutmeg and cinnamon. Many of the grains also showed signs of deformation, which suggests that they were damaged from grinding and look similar to the starch granules found in modern curry powder.Advertisement
“This finding strongly suggests that the ancient inhabitants of Oc Eo utilised turmeric, ginger and other spices like cinnamon, clove and nutmeg as essential ingredients in their culinary practices, highly likely in the preparation of curry,” says Hung.
A sandstone grinding slab found at Oc Eo in Vietnam, on which traces of spices were identifiedKhanh Trung Kien Nguyen
Maritime trading routes between South-East Asia and south Asia were established more than 3000 years ago, with spices such as nutmeg and clove coming from Indonesia and others such as turmeric and cinnamon from south Asia.
Stone grinding tools first appeared in South-East Asia 2000 to 3000 years ago, along with other cultural elements originating in south Asia, such as Indian ornaments and religious monuments. Therefore, it is highly probable that these tools, spices and recipes were introduced to the region by migrants or travellers from south Asia, says Hung. The spices found at Oc Eo probably came from traders, but could have been grown locally from seeds brought by traders, say the researchers.
The findings provide valuable information about the dietary habits of South-East Asian societies at the time and also offer a glimpse into the cultural and trading connections between different regions over thousands of years, says Hung.

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