Tag Archives: tree of life

Human activity might undo more than 50 billion years of evolution

Baby pangolin. Credit: Yingboon Chongsomchai, ZSL.

Researchers from the Zoological Society of London (ZSL) and Imperial College have completed one of the most comprehensive analyses of the evolutionary history of terrestrial vertebrates and how countless species of amphibians, birds, mammals, and reptiles are being impacted by human activity — as expected, it’s not pretty at all.

“We found that the most important areas for global evolutionary history are facing much higher levels of human pressure than we expected, with 3/4th of the most diverse regions under high or very high human pressure. Conversely, just 5% of these critical areas are under little or no human pressure,” lead author Rikki Gumbs, of ZSL’s EDGE of Existence programme and the Science and Solutions for a Changing Planet Doctoral Training Partnership at Imperial College London, told ZME Science.

“When we quantified the scale of impact by human activities across the tree of life for amphibians, birds, and mammals, we found it to be incomprehensibly large: close to 50 billion years of unique evolutionary history is at risk of being lost forever due to humanity’s actions. Numbers that large are typically associated with astrophysics, not biodiversity.”

This was the first time that researchers have investigated how areas with important concentrations of evolutionary distinct and threatened species are being impacted by human activity.

Although it’s not secret that humans are driving many species extinct through habitat encroachment, hunting, fishing, and wildlife trade, the new study has revealed important insights that animal conservation may have missed before.

For instance, the authors conclude that many regions of the world that are home to the greatest amount of unique evolutionary heritage are also some of the most affected by human footprints. These include the Caribbean, the Western Ghats in India, and large regions of Southeast Asia.

In order to figure out the amount of evolutionary history currently threatened with extinction, the researchers turned to data relevant for around 25,000 species.

“We embarked on this study for several reasons. First, we understand that the tree of life is an extremely important component of the world’s biodiversity. It is linked to ecosystem productivity and to future benefits for humanity. Identifying what species and regions across the planet are highly evolutionarily unique and facing intense human pressure will allow us to target conservation efforts to better understand and conserve these unique and amazing species and places,” Gumbs said.

The Mary River turtle (Elusor macrurus) is an endangered short-necked turtle that is endemic to the Mary River in south-east Queensland, Australia. Credit: ZSL, Chris Van Wyk.

After combing through hundreds of gigabytes of data and making sense of huge datasets, Gumbs and colleagues were stunned by the results of their calculations.

“I still remember having to double-check my calculations when I found that we stand to lose close to 50 billion years of evolutionary history across amphibians, birds, mammals, and reptiles! I counted and re-counted the number of zeroes to make sure I wasn’t making a mistake before emailing my supervisor. Unfortunately for the tree of life, my estimates weren’t a mathematical error,” he recounted.

All living things on Earth can trace their descent back to a common ancestor. However, smaller groups of species can also trace their ancestry back to common ancestors, often a much more recent one.

Phylogenetic trees map these relationships, with common ancestors acting as branch points. Biologists draw the branching tree of life by grouping species by shared characteristics that illustrate the degree of relatednesses, such as external morphology (shape/appearance), internal anatomy, behaviors, biochemical pathways, DNA and protein sequences, and even the characteristics of fossils.

However, not all branches are equal. Some are broad and rich, encompassing many living related species, while others are short and stubby. Then, there are branches in the tree of life where only a single species is still left — when that species dies, the entire lineage disappears with it.

For instance, the researchers found that human activity is threatening groups of closely-related species that share long branches of the tree of life, such as pangolins and tapirs. However, some of the species that face extinction belong on the tail end of extremely long branches. These include the ancient Chinese crocodile lizard (Shinisaurus crocodilurus), the Shoebill (Balaeniceps rex), a gigantic bird that stalks the wetlands of Africa, and the Aye-aye (Daubentonia madagascariensis), a nocturnal lemur with large yellow eyes and long spindly fingers. 

The shoebill (Balaeniceps rex) also known as whalehead, whale-headed stork, or shoe-billed stork, is a very large stork-like bird. Credit: ZSL, Claudia Gray.

As such, the study is offering a framework for conservation that highlights priority species, such as the punk-haired Mary River turtle (Elusor macrurus), the Purple frog (Nasikabatrachus sahyadrensis), and the Numbat (Myrmecobius fasciatus)

“All species are worth saving! Sadly, in conservation, we lack the resources to actually achieve this, given our huge impacts on the environment. Prioritising species based on their evolutionary uniqueness, as we do at the EDGE of Existence programme, should be seen as a complementary approach to other conservation efforts, such as preserving entire ecosystems and species critical to their environments that are perhaps not evolutionarily unique. However, as evolutionary history (as Phylogenetic Diversity) is a fundamental measure of biodiversity, saving species that are responsible for greater amounts of unique evolutionary history than others does represent a greater gain in the conservation of biodiversity at a global scale,” Gumbs said.

The reality may be even more depressing as this analysis is just the tip of the iceberg. The study did not account for the decline in biodiversity for insects (more than 40% of which are threatened by extinction), flowers, or fungi.

“Our work focuses on the world’s terrestrial vertebrates: amphibians, birds, mammals, and reptiles. We used these groups as they have the best data available. However, these species are just the tip of the iceberg in terms of the current extinction crisis. We don’t know how humanity is threatening the entire tree of life, from insects and fish to fungi and flowers. Hopefully we can gather enough data to expand our work to incorporate other groups of animals and plants that are also facing huge losses during this crisis,” Gumbs said.

“We hope this research can inspire others to develop a better understanding of, and provide effective conservation for, the species we highlight as priorities before it’s too late. This study highlights just how harmful our current global system is to the future of biodiversity, and we need to enact change at all levels before it’s too late for the world’s most unique and threatened diversity.”

The findings were reported in the journal Nature Communications.

The newest and most refined tree of life. Clusters of bacteria (left), uncultivable bacteria called 'candidate phyla radiation' (center, purple) and, at lower right, the Archaea and eukaryotes (green), including humans. Credit: Lawrence Berkeley National Laboratory

Tree of life expanded to match reality: two third of all diversity is bacterial

Most of the life we see around us — plants, animals, humans and other eukaryotes — actually comprise a tiny minority of the planet’s biodiversity. The rulers of this planet are actually bacteria and Archaea. A new research which includes genome sequencing data from over 1,000 new organisms produced a refined tree of life that better matches reality. In this expanded tree of life  two-thirds of all diversity on Earth is bacterial, while nearly a third is Archaea.

The root of life

The newest and most refined tree of life. Clusters of bacteria (left), uncultivable bacteria called 'candidate phyla radiation' (center, purple) and, at lower right, the Archaea and eukaryotes (green), including humans. Credit: Lawrence Berkeley National Laboratory

The newest and most refined tree of life. Clusters of bacteria (left), uncultivable bacteria called ‘candidate phyla radiation’ (center, purple) and, at lower right, the Archaea and eukaryotes (green), including humans. Credit: Lawrence Berkeley National Laboratory

“The tree of life is one of the most important organizing principles in biology,” said Jill Banfield, a UC Berkeley professor of earth and planetary science and environmental science, policy and management, in a press release. “The new depiction will be of use not only to biologists who study microbial ecology, but also biochemists searching for novel genes and researchers studying evolution and earth history.”

The tree of life was first sketched by none other than Charles Darwin in 1837. Darwin developeda convenient way to represent the relation between plants, mammals or bacteria. His idea was to draw a tree where the tip of the twigs represents living life on Earth today while the branches connecting the twigs to the trunk represent an evolutionary relationship between the organisms. It can get more complicated. For instance, a branch that forks into two twigs near the tip of the three means that these organisms share a recent common ancestor. If the fork is closer to the trunk, this evolutionary split occurred in the distant past.

In 1977, one of the most appreciated biologists you’ve likely never heard of, Carl Woese, published a groundbreaking paper that proved that Archaea wasn’t a minor twig on the tree of life, but a new main branch. Up until then, the tree of life was separated into two main domains: Bacteria and Eukarya. Now, there are three.

Archea are very similar to bacteria visually, but they have  genes and several metabolic pathways that are more closely related to those of eukaryotes, notably the enzymes involved in transcription and translation.

Diagrammatic representation of the divergence of modern taxonomic groups from their common ancestor. Image: Wikimedia

Diagrammatic representation of the divergence of modern taxonomic groups from their common ancestor. Image: Wikimedia

Later, Woese published a refined tree of life that biologists consider transformative. The tree of life contains all three domains of life and, most importantly, it groups organisms using DNA. Up until Woese came along, biolologists used the  shapes of microbes—their morphologies—and how they turned food into energy—their metabolisms—to sort them into bins. The impact was monumental.

In 2012 Woese passed, but his legacy lives on and is constantly refined towards perfection. Banfield and colleagues, for instance, are part of a new wave of biologists that can make extraordinary discoveries where Woese and other failed because they lacked access to technology.

Many organisms can not be cultured in the lab because they can’t live on their own. Instead, they have to get their energy from other organisms acting as parasites, symbiotic organisms or scavengers. This includes a group of bacteria called “candidate phyla radiation”. The new analysis suggests that this group forms a major branch in the tree of life and  contain around half of all bacterial evolutionary diversity.

“What became really apparent on the tree is that so much of the diversity is coming from lineages for which we really only have genome sequences,” she said. “We don’t have laboratory access to them, we have only their blueprints and their metabolic potential from their genome sequences. This is telling, in terms of how we think about the diversity of life on Earth, and what we think we know about microbiology.”

“The candidate phyla radiation has as much diversity within it as the rest of the bacteria combined,” Banfield said.

The new tree of life shows that one-third of all biodiversity comes from bacteria, one-third from uncultivable bacteria and a bit less than one-third from Archaea and eukaryotes. The things that you deem most recognizable — plants, insects, mammals, even dinosaurs — are just a drop in the ocean.

“This incredible diversity means that there are a mind-boggling number of organisms that we are just beginning to explore the inner workings of that could change our understanding of biology,” said co-author Brett Baker, formerly of Banfield’s UC Berkeley lab but now at the University of Texas, Austin, Marine Science Institute.

Reference: Laura A. Hug, Brett J. Baker, Karthik Anantharaman, Christopher T. Brown, Alexander J. Probst, Cindy J. Castelle, Cristina N. Butterfield, Alex W. Hernsdorf, Yuki Amano, Kotaro Ise, Yohey Suzuki, Natasha Dudek, David A. Relman, Kari M. Finstad, Ronald Amundson, Brian C. Thomas, Jillian F. Banfield. A new view of the tree of life. Nature Microbiology, 2016; 16048 DOI: 10.1038/nmicrobiol.2016.48

Scientists develop new tree of life, with all known organisms

After years of analyzing and reclassifying some 2.3 million species, a group of international researchers from eleven institutions were able to create the most advanced and up to date tree of life. This all inclusive tree is actually pieced together by compiling thousands of other, smaller trees.

Image Credit: opentreeoflife.org

Of course, new species are being discovered all the time and we still don’t know many of the species living on Earth, so this attempt is not exactly exhaustive, but it’s the closest thing. The tree started by encompassing 500 smaller trees from previously published studies; everything had to be digitized and translated into a unique database, and this was quite the daunting task. Much to the dismay of the researchers, they found that only one out of six studies in 100 journals published between 2000 and 2012 had their data available in a digital format. While most studies provided some type of list, translating a PDF into a database is highly time consuming. However, some provided no background data at all.

Even this is only the first attempt:

“This is the first real attempt to connect the dots and put it all together,” said Karen Cranston of Duke University, the research’s principal investigator, in a press release. “Think of it as Version 1.0.” Cranston also noted, “It’s critically important to share data for already-published and newly-published work if we want to improve the tree.”

But the tree of life is not just for show – the tree of life will also provide a number of functions, including tracing the origins of some species, improving agricultural techniques and even providing information for new drugs.

You can view the data by yourself, for free, by visiting their website: Open Tree of Life.

Comb jellies could be the earliest ancestors of all animals

With their eerie, translucent and soft bodies, their translucent and intricate shapes and bizarre bioluminescent displays, comb jellies are among the biggest beauties and mysteries in the oceans. Now, according to a biologist from Vanderbilt University, these delicate marine predators have another important story to tell about the origin of animals; a 550 million year old story.

Ctenophore Bolinopsis infundibulum. (Wikipedia Commons)

Comb jellies are part of a genus called Ctenophora (Greek for ‘comb bearers’). You wouldn’t guess it, but Ctenophores, variously known as comb jellies, sea gooseberries, sea walnuts, or Venus’s girdles, are voracious predators.

Antonis Rokas reflected on the significance of the first successful sequencing of the genome of the genus, conducted by Andreas Baxevanis at the National Human Genome Research Institute – the sea walnut, an aggressive species that invaded the Black Sea in the 1980s. Based on a very thorough analysis of the sea walnut genome, Baxevanis and his team came to the conclusion that ctenophores are the oldest relative of the entire animal family, including humans.

Sea walnut at the Boston Aquarium. (Wikipedia Commons)

His results seem pretty convincing, but the only problem is that the study contradicts several other convincing studies as well. As a matter of fact, not one, but several other studies grouped comb jellies together with jellyfish, and concluded that sponges are the oldest animal relative, despite their sedentary nature.

But Rokas, who has studied many directly conflicts between well-documented phylogenetic studies says it is not really a surprise to find contradictory tree-of-life studies. The branchings that gave rise to the lineages that eventually became the sponges, ctenophores and jellyfish took place in a narrow window of time a long time ago – it’s these conditions that are very hard to map.

But even if he is right or wrong, it’s clear that we have to consider the addition of comb jellies to existing knowledge of the earliest animals and their closest relatives.

You can’t really choose your relatives or ancestors… but when it comes to it, I’d choose a ctenophore over a sponge.

Via Vanderbilt University.