Tag Archives: lineage

Huskies belong to an almost 10,000-year-old lineage

New research at the University of Copenhagen (UoC) finds that sled dogs are a much older lineage than previously believed. Their ancestors, the team reports, worked and lived with humans in the Arctic for almost 10 millennia.

Image via Pixabay.

Man’s best friend is almost ubiquitous in society today as pets, service, and working animals. We know their origin story in large strokes — dogs evolved from domesticated wolves — but the exact details of this process are still unclear.

The team at the UoC’s Faculty of Health and Medical Sciences, in collaboration with researchers from Greenland and Barcelona, analyzed the genomes of ancient and modern sledge dog species to better determine their history. Such dogs evolved much earlier than assumed, they explain.

Snow doggos

“We have extracted DNA from a 9,500-year-old dog from the Siberian island of Zhokhov, which the dog is named after,” says co-lead author Mikkel Sinding, a Ph.D. student at the Globe Institute in Barcelona.

“Based on that DNA we have sequenced the oldest complete dog genome to date, and the results show an extremely early diversification of dogs into types of sled dogs.”

Modern breeds such as the Siberian Husky, the Alaskan Malamute, and the Greenland sled dog share an important amount of genes with the Zhokhov dog. This suggests the sled dog lineage is at least as old as it and remained quite isolated from other populations of wolves and dogs for the most part.

As part of their study, the team also sequenced the genomes of a 33,000-year-old Siberian wolf and ten modern Greenlandic sled dogs. These were there compared to genetic data from modern dogs and wolves across the globe.

“We can see that the modern sledge dogs have most of their genomes in common with Zhokhov. So, they are more closely related to this ancient dog than to other dogs and wolves,” says Sinding.

“But not just that — we can see traces of crossbreeding with wolves such as the 33,000-year-old Siberian wolf — but not with modern wolves. It further emphasises that the origin of the modern sledge dog goes back much further than we had thought.”

Historical population data also shows that Greenland sled dogs were stable in numbers up to around 850 years ago when they went through a “bottleneck”. This coincides with the Inuits colonizing Greenland, the authors explain. This points to the lineage being isolated in the area before and after humans entered their ecosystem.

While modern sledge dogs share more of the genetic makeup of the Zhokhov dog than other modern breeds, we still don’t know when this split in lineages took place, or why. However, Greenland sledge dogs are the most genetically-remote from other modern dog species.

Some of the genetic differences between these two groups include genetic adaptations for a starch- and sugar-rich diet that the sledge dogs lack. Instead, their genetics favor diets with a lot of fat, similar to that of Arctic natives or polar bears.

“This emphasises that sledge dogs and Arctic people have worked and adapted together for more than 9,500 years. We can also see that they have adaptations that are probably linked to improved oxygen uptake, which makes sense in relation to sledding and give the sledding tradition ancient roots,” concludes Associate Professor Shyam Gopalakrishnan, the other co-lead author.

The paper “Arctic-adapted dogs emerged at the Pleistocene–Holocene transition” has been published in the journal Science.

Bacteria lip print.

Bacteria species, too, can become extinct — and they do so quite often

Evolution is ruthless even with its tiniest creations.

Bacteria lip print.

Image credits Bnummer / Wikimedia.

New research led by researchers from the University of British Columbia (UBC) reports that bacteria also die off — and they do so at substantial rates. The findings go against the grain of the widely-held notion that bacterial species, owing to their very large populations, rarely go extinct.

To kill a M. ocking bacteria

Bacteria are, by far, one of the most prolific and successful bits of life that evolution spawned on our planet. They’re incredibly hardy, very good at drawing energy from their environments, and they reproduce with a vengeance. These tiny critters are so resilient and numerous, in fact, that most scientists took it as a given that bacteria species very rarely go extinct. However, new research suggests that this isn’t the case.

The team sequenced DNA information from 448,112 different bacterial species and drew on 60 previous environmental studies to create the most comprehensive bacteria evolutionary tree, which includes the majority of bacterial species over the past billion years. To get an idea of bacteria’s evolutionary history, they drew on the traces that speciation (differentiation of new species through evolution) leaves in the genetic makeup of these bacterial lineages.

The team estimates that there are around 1.4 to 1.9 different bacterial phyla (lineages) gracing our planet today. They were also able to estimate how that number varied over time: they report that anywhere between 45,000 to 95,000 phyla became extinct over the last million years.

“Bacteria rarely fossilize, so we know very little about how the microbial landscape has evolved over time,” says Stilianos Louca, lead researcher of the study. “Sequencing and math helped us fill in the bacterial family tree, map how they’ve diversified over time, and uncover their extinctions.”

It’s an impressive number. But, despite these relatively high extinction rates (which the team notes were quite steady over time), bacteria have kept diversifying exponentially throughout history. As a group, they also managed to weather planet-wide mass extinction events — those abrupt events that periodically cull plant and animal species — with very few losses. All in all, while the current number of bacterial lineages today is definitely impressive, “it’s only a tiny snapshot of the diversity that evolution has generated over Earth’s history,” Louca adds.

“This study wouldn’t have been possible 10 years ago,” says Michael Doebeli, senior author of the paper and a UBC mathematician and zoologist. “Today’s availability of massive sequencing data and powerful computational resources allowed us to perform the complex mathematical analysis.”

Next, Louca says he and his team plan to determine how the physiological properties of bacteria evolved over time. A particular point of interest for them is determining whether their ecological diversity has increased in tow with their taxonomic diversity — i.e. if they spread to new types of environments and roles in those environments as the total number of species increased. If so, this would suggest that even organisms as ancient and simple as bacteria can still find new roles in nature.

The paper “Bacterial diversification through geological time” has been published in the journal Nature ecology and evolution.

Comb jellie, the phylum Ctenophora, may have been the first creatures on Earth. Credit: Wikimedia Commons.

Comb Jellies may have been the first animals ever

Since 2008, scientists have debated which of the two came first: the sponge (Porifera) or the comb jelly (Ctenophora). A new thorough genetic analysis suggests the latter was Earth’s first animal out of which all other creatures evolved.

Editor’s note: while very similar, comb jellies technically aren’t jellyfish (subphylum Ctenophora vs phylum Medusozoa). The term ‘jellyfish‘ in this article refers to comb jellies. Thanks to Wastrel Way for pointing it out.

Comb jellie, the phylum Ctenophora, may have been the first creatures on Earth. Credit: Wikimedia Commons.

Comb jelly, the phylum Ctenophora, may have been the first creatures on Earth. Credit: Wikimedia Commons.

For more than a century, biologists generally agreed that the first creature to evolve on this planet was a sponge because it’s such a simple creature. The sponge doesn’t have circulatory, nervous, or digestive systems, and only needs water to flow through its pores to survive. After DNA was discovered, and much later when modern genetic sequencing tools appeared, the status of the sponge as the first animal in the world seemed even more cemented. One previous genetic analysis, for instance, showed most genes involved in complex processes are present in sponges. 

The sponge, however, isn’t the only ancient animal at the bottom of all modern creature’s lineage. In 2008, a family-tree study pointed out that the comb jellies came before the sponge, and ever since scientists have been locked in a debate. A recent study which attempted to resolve the early diversification of animal lineages used a massive 1,719-gene dataset with dense taxonomic sampling and found evidence supporting the idea that sponges represent the sister group to all other animals.

While impressive, Antonis Rokas, a biology professor at Vanderbilt University, cautions that such ‘big data’ analyses can still pose phylogenomic contradictions.

“This has worked extremely well in 95 percent of the cases, but it has led to apparently irreconcilable differences in the remaining 5 percent,” Rokas said in a statement.

In a new paper published in Nature Ecology & EvolutionRokas and colleagues employed a new approach to settle 18 controversial phylogenetic relationships, among them the ‘sponge vs comb jellyfish’ debate. In total, the study included seven relationships from animals, five from plants, and six from fungi in order to figure out why so many studies have come up with such conflicting results. To get to the bottom of things, the researchers painstakingly compared the individual genes of the leading contenders in each relationship. That’s hundreds of thousands of genes.

“In these analyses, we only use genes that are shared across all organisms,” Rokas said. “The trick is to examine the gene sequences from different organisms to figure out who they identify as their closest relatives. When you look at a particular gene in an organism—let’s call it A—we ask if it is most closely related to its counterpart in organism B? Or to its counterpart in organism C? And by how much?”

By determining which genes weighed more for a particular hypothesis, like ‘comb jelly came first’, and by labeling the resulting differences as a ‘phylogenetic signal’, the team determined that the comb jelly has significantly more genes which support its ‘first to diverge’ status than the sponge.

Besides jellyfish vs sponges, the researchers also addressed other phylogenetic conflicts like whether crocodiles are more related to birds or turtles. Using the same method, the researchers found 74 percent of the shared genes indicate that crocodiles and birds form sister lineages while turtles are just close cousins.

As to why previous efforts turned out to be so controversial, Rokas suggests the statistical methods used by evolutionary biologists are influenced by ‘strongly opinionated genes’. Only a handful of such genes, which have a strong phylogenetic signal for one of the specific hypotheses, pop up in studies, but these are enough to skew results. For instance, in the case of another controversy surrounding flowering plants and modern birds, the researchers found that removing a single opinionated gene flipped the results from one candidate to another. In this particular case, the team published an inconclusive result either because the available data is inadequate or because the diversification occurred too rapidly to resolve.

“We believe that our approach can help resolve many of these long-standing controversies and raise the game of phylogenetic reconstruction to a new level,” Rokas said.

Of course, that’s not to say this is the final word on the matter. As outlined earlier, it was only in March that a comprehensive genetic analysis gave credence to sponges as the ‘first to diverge’ in favor of the jellyfish. It’s likely that the two will switch roles multiple times before biologists reach a satisfying method. It’s amazing, however, that out of the millions of species that lived on Earth we’re able to single out only two main candidates. That, in itself, is a testimony to how powerful science is.