Reference Human Genome Almost Complete

 

Work remains to finalize the reference genome (the Y chromosome still needs to be finished) but researchers are close to finally sequencing every last nucleotide of human DNA.

Ever since the launch of the Human Genome Project more than 30 years ago, genetic sequencing technologies and data-processing pipelines have been getting faster, cheaper and more precise, allowing researchers to sample, sequence and compare more genomes with every passing year.

But huge chunks of DNA – amounting to around 8 percent of the human genome – were still missing from the most recent reference sequence that scientists use as a template to assemble newly-sequenced DNA samples.

Now, scientists have pieced together those parts of the human genome which have long been 'unsequenceable' to assemble the most complete reference genome to date, sharing their findings in a collection of six papers, published in the journal Science.

Read more here and here.

DNA Study of Caribbean Islanders Yields Surprises

 

These pieces reveal a range of styles and date to around 1200 A.D. 

(Corinne Hofman and Menno Hoogland / Florida Museum of Natural History)

New DNA studies have clarified migrations to islands of the Caribbean, but also raise additional questions. One question is why the European explorers of those island believed the native population to be much higher than the studies indicate?

This report on a technique developed by Harald Ringbauer, a postdoctoral fellow in the Reich Lab, explains that shared segments of DNA were used to estimate past population size, and showed that only about 10,000 to 50,000 people were living on two of the largest islands, Hispaniola and Puerto Rico, shortly before European arrival.

"While the heat and humidity of the tropics can quickly break down organic matter, the human body contains a lockbox of genetic material: a small, unusually dense part of the bone protecting the inner ear. Primarily using this structure, researchers extracted and analyzed DNA from 174 people who lived in the Caribbean and Venezuela between 400 and 3,100 years ago, combining the data with 89 previously sequenced individuals.

The team, which includes Caribbean-based scholars, received permission to carry out the genetic analysis from local governments and cultural institutions that acted as caretakers for the human remains. The authors also engaged representatives of Caribbean Indigenous communities in a discussion of their findings.

The genetic evidence offers new insights into the peopling of the Caribbean. The islands' first inhabitants, a group of stone tool-users, boated to Cuba about 6,000 years ago, gradually expanding eastward to other islands during the region's Archaic Age. Where they came from remains unclear -- while they are more closely related to Central and South Americans than to North Americans, their genetics do not match any particular Indigenous group."

The new study suggests the Caribeean islands were first populations by two waves. A group of migrants almost totally replaced the islands’ original population. Only 3 of the individuals sampled showed ancestry of two distinct populations.

Dr. William F. Keegan, whose work in the Caribbean spans more than 40 years, contributed to the study. He is curator at the Florida Museum of Natural History and co-senior author of the study. "The methods David's team developed helped address questions I didn't even know we could address."

The Arawak-speakers who arrived on these islands from northeast South America introduced ceramics about 2500 years ago. 

"During the Ceramic Age, Caribbean pottery underwent at least five marked shifts in style over 2,000 years. Ornate red pottery decorated with white painted designs gave way to simple, buff-colored vessels, while other pots were punctuated with tiny dots and incisions or bore sculpted animal faces that likely doubled as handles. Some archaeologists pointed to these transitions as evidence for new migrations to the islands. But DNA tells a different story, suggesting all of the styles were developed by descendants of the people who arrived in the Caribbean 2,500-3,000 years ago, though they may have interacted with and took inspiration from outsiders.

"That was a question we might not have known to ask had we not had an archaeological expert on our team," said co-first author Kendra Sirak, a postdoctoral fellow in the Reich Lab. "We document this remarkable genetic continuity across changes in ceramic style. We talk about 'pots vs. people,' and to our knowledge, it's just pots." 

Read the full report here: Ancient DNA retells the story of Caribbean's first people, with a few plot twists; Pre-Columbian Pottery in the West Indies; Old World Migrations to the Americas

Two New Species of Cyanobacteria

In the past, microorganisms called "cyanobacteria" were grouped by looking at their shape under a microscope. Now researchers also use DNA to classify them.

Researchers collected 26 samples of water, soil, and bone for analysis, from varied cold-weather locations around the globe (Antarctica, the Arctic, Greenland, Sweden, and Germany), each suspected to contain different types of cyanobacteria in the genus Phormidesmis. Phormidesmis priestleyi is a cyanobacterium found throughout the cold regions.

They grew Phormidesmis from each sample in the laboratory, and then analyzed each using a heavy-duty microscope to characterize their shapes and compare them to known cyanobacterial cells.

DNA is a very long molecule made of four “bases” and the order of those bases is unique for each living thing. The cyanobacteria’s DNA was then extracted and isolated from each sample and the base order for each DNA strand was determined. This is referred to as genome sequencing. The authors sequenced a gene known as the “16S rRNA gene” that is commonly used for classification of bacteria. Those gene sequences were compared to other gene sequences in large public databases of already-identified sequences to see if there was a match.

Based on these DNA results, the researchers were able to provide better classification of cyanobacteria. They also unexpectedly discovered two new species of cyanobacteria based on visual observations and DNA testing. These new organisms were named Phormidesmis arctica and Phormidesmis communis, and the scientists reclassified one species that was previously in the genus Leptolyngbya to Phormidesmis. This species is now Phormidesmis nigrescens.

A new genus was also suggested, Leptodesmis, as the genome is not easily recognizable by its shape and appears to belong to more than one taxonomic group. The importance of properly classifying all life forms gives scientists a better understanding of the interrelationships of these organisms and is the necessary basis for other studies. Humankind must understand the smallest living organisms in order to fully understand all living things.

Related reading: DNA Helps Identify a New Type of Bacteria: New Genome Reveals How Arctic Microbes Survive the Cold

Diversity Among Paleo-Siberians

Two children's milk teeth buried deep in a remote archaeological site in north eastern Siberia have revealed a previously unknown group of people lived there during the last Ice Age.

The finding was part of a wider study which also discovered 10,000 year-old human remains in another site in Siberia are genetically related to Native Americans -- the first time such close genetic links have been discovered outside of the US.

The international team of scientists, led by Professor Eske Willerslev who holds positions at St John's College, University of Cambridge, and is director of The Lundbeck Foundation Centre for GeoGenetics at the University of Copenhagen, have named the new people group the 'Ancient North Siberians' and described their existence as 'a significant part of human history'.

The DNA was recovered from the only human remains discovered from the era -- two tiny milk teeth -- that were found in a large archaeological site found in Russia near the Yana River. The site, known as Yana Rhinoceros Horn Site (RHS), was found in 2001 and features more than 2,500 artefacts of animal bones and ivory along with stone tools and evidence of human habitation. (Read more here.)


Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas. (From here.)

Some Ancient North Siberians journeyed onto the Bering land bridge that connected Asia to North America around 30,000 years ago. Mating with East Asians who had also moved to the land bridge produced a genetically distinct population, dubbed Ancient Palaeo-Siberians by the researchers. As the climate became milder after 20,000 years ago, some of the Ancient Palaeo-Siberian population returned to northeastern Siberia, replacing the Yana crowd.

Other Ancient Palaeo-Siberians trekked from the land bridge into North America, the researchers say. Some of this group’s descendants returned to Siberia by sea between 11,000 and 4,000 years ago, after rising waters had submerged the bridge. Many Siberians today have descended from that population, referred to as Neo-Siberians by the scientists.

A nearly 10,000-year-old Siberian man’s DNA enabled the researchers to identify genetic links between Ancient Palaeo-Siberians and present-day native communities in both modern Siberia and North America. (From here.)

Related reading: Ket-Navajo Linguistic Connection; Characterizing the genetic history of admixture across inner Eurasia