How snakes lost their limbs

This February 2018 video says about itself:

90 million years ago, an ancient snake known as Najash had…legs. It is by no means the only snake to have limbs either. But what’s even stranger: we’re not at all sure where it came from.

From the Fundação de Amparo à Pesquisa do Estado de São Paulo in Brazil:

Research explains how snakes lost their limbs

The study is part of an effort to understand how changes in the genome lead to changes in phenotypes

February 6, 2019

Snakes and lizards are reptiles that belong to the order Squamata. They share several traits but differ in one obvious respect: snakes do not have limbs. The two suborders diverged more than 100 million years ago.

Identification of the genetic factors involved in this loss of limbs is a focus of the article “Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution” published by Juliana Gusson Roscito and collaborators in Nature Communications.

Another equally interesting focus of the article is eye degeneration in certain subterranean mammals.

“We investigated these two cases in order to understand a much more general process, which is how genome changes during evolution lead to phenotype changes,” Roscito told.

Currently working as a researcher at the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden, Germany, Roscito has been a postdoctoral fellow in Brazil and a research intern abroad with São Paulo Research Foundation — FAPESP’s support. Her postdoctoral scholarship was linked to the Thematic Project “Comparative phylogeography, phylogeny, paleoclimate modeling and taxonomy of neotropical reptiles and amphibians,” for which Miguel Trefaut Urbano Rodrigues is the principal investigator under the aegis of the FAPESP Research Program on Biodiversity Characterization, Conservation, Restoration and Sustainable Use (BIOTA-FAPESP).

Rodrigues is a Full Professor at the University of São Paulo’s Bioscience Institute (IB-USP) in Brazil and supervised Roscito’s postdoctoral research. He is also a coauthor of the recently published article.

“The research consisted of an investigation of the genomes of several species of vertebrates, including the identification of genomic regions that changed only in snakes or subterranean mammals, while remaining unchanged in other species that have not lost their limbs or have normal eyes,” Roscito said.

“In mammals with degenerated visual systems, we know several genes have been lost, such as those associated with the eye’s crystalline lens and with the retina’s photoreceptor cells. These genes underwent mutations during the evolutionary process. Eventually, they completely lost their functionality, meaning the capacity to encode proteins. But that’s not what happened to snakes, which haven’t lost the genes associated with limb formation. To be more precise, the study that sequenced the genome of a snake did detect the loss of one gene, but only one. Therefore, the approach we chose in our research consisted of investigating not the genes but the elements that regulate gene expression.”

Gene expression depends on regulatory elements for the information the gene contains to be transcribed into RNA (ribonucleic acid) and later translated into protein. This process is regulated by cis-regulatory elements (CREs), which are sequences of nucleotides in DNA (deoxyribonucleic acid) located near the genes they regulate. CREs control the spatiotemporal and quantitative patterns of gene expression.

“A regulatory element can activate or inhibit the expression of a gene in a certain part of the organism, such as the limbs, for example, while a different regulatory element can activate or inhibit the expression of the same gene in a different part, such as the head. If the gene is lost, it ceases to be expressed in both places and can often have a negative effect on the organism’s formation.

However, if only one of the regulatory elements is lost, expression may disappear in one part while being conserved in the other,” Roscito explained.

Tegu lizard

From a computational standpoint, CREs are not as easy to identify as genes. Genes have a characteristic syntax, with base pairs that show where the genes begin and end. This is not the case for CREs, so they have to be identified indirectly. This identification is normally based on the conservation of DNA sequences among many different species.

“To detect the divergence of specific sequences in snakes, it’s necessary to compare the genomes of snakes with the genomes of various reptiles and other vertebrates that have fully developed limbs. Genome sequences for reptiles with well-developed limbs are scarce, so we sequenced and assembled the genome of the fully limbed tegu lizard, Salvator merianae. This is the first species of the teiid lineage ever sequenced,” the authors said.

“Using the tegu genome as a reference, we created an alignment of the genomes of several species, including two snakes (boa and python), three other limbed reptiles (green anole lizard, dragon lizard and gecko), three birds, an alligator, three turtles, 14 mammals, a frog, and a coelacanth. This alignment of 29 genomes was used as the basis for all further analyses.”

The researchers identified more than 5,000 DNA regions that are considered candidate regulatory elements in several species. They then searched the large database using ingenious technical procedures that are described in detail in the article and obtained a set of CREs the mutation of which may have led to the disappearance of limbs in the ancestors of snakes.

“There are several studies concerning a well-known regulatory element that regulates a gene that, when modified, causes various defects in limbs. Snakes have mutations in this CRE. In a study published in 2016, the mouse CRE was replaced with the snake version, resulting in practically limbless descendants. This was a functional demonstration of a mechanism that may have led to limb loss in snakes. However, this CRE is only one of the regulatory elements for one of several genes that control limb formation,” Roscito said.

“Our study extended the set of CREs. We showed that several other regulatory elements responsible for regulating many genes have mutated in snakes. The signature is far more comprehensive. An entire signaling cascade is affected.”


Worldwide students’ strikes against climate change

This 14 November 2018 video says about itself:

Climate Strike: Heeding Call of Greta Thunberg, Polish Students Walk Out of Class

Fifteen-year-old Swedish climate activist Greta Thunberg has called for a global climate strike today to protest inaction at the U.N. climate summit. Greta made international headlines after she refused to go to school in August and began a School Strike for Climate. Greta made the call for today’s strike in a video posted on Twitter.

Translated from Dutch NOS TV today:

Schülerstreik and Fridays for Future: young people play truant for the climate

Tomorrow, organizers hope to have a climate protest with thousands of students at the Malieveld in The Hague.

Although in the Netherlands, in particular, people look at the passion about the climate of which has suddenly flared up in Belgium, in recent times young people worldwide have been on strike for a better climate. They interrupted their school day in Germany, Australia and Switzerland. An overview.

The Greta effect

First, their joint inspiration: the 16-year-old climate activist Greta Thunberg from Sweden. She is now an icon for young people around the world.

As a little girl, Greta was already worried about the greenhouse effect and did not understand why adults were barely mentioning it. Inspired by demonstrations by US American students against the use of firearms, she tried to persuade classmates to go on strike for the climate.

But when nobody wanted to participate, she decided to take action herself: three weeks before the Swedish elections in September she stood demonstratively in front of the parliament building. With her school bag and a piece of cardboard, with the text ‘School strike for the climate’. …

Greta Thunberg, SVT photo

The biggest demonstration in Scandinavia was last Friday, on 1 February. Then students went on strike in different cities in Sweden, Denmark, Norway, Finland and even Greenland and the Faroe Islands.

Greta Thunberg stayed in front of the parliament every day during school hours, until the Swedish elections. After that she was only allowed to demonstrate by her parents on Fridays – and she still does. She gave speeches during the climate summit in Poland and at the World Economic Forum in Davos. Now she is considering to take a one-year break from school and to be occupied full-time with climate activism.


At the end of November Down Under, thousands of students were leaving their classes to demand action from the government.

The Prime Minister of Australia, Scott Morrison, had urged children earlier that week not to participate in the actions and to go to school to learn. “We also learn from this action, even though it is during school time!” was their response. “We can not stay silent until we are old enough to vote.”

One of the organizers was 14-year-old Harriet O’Shea. In a letter to The Guardian, Harriet tells that she lives in the countryside of Victoria, and has seen in her life the effects of drought, forest fires and extreme weather on society. “We were evacuated once when a forest fire came to our town, which was scary, but it is something that will happen more and more often.”

The young people promised to continue demonstrating until something would change in Australia. …


Greta Thunberg also inspired a lot of students in Germany. “It started with tufts of high school students and university students who canceled their classes on Friday”, says correspondent Judith van de Hulsbeek. “But last week, tens of thousands of students went out on the streets all over Germany on Friday.” Schwänzen, truancy in German, for the climate.

One of the faces of the Schülerstreik is Jakob Blasel (18) from the North German town Kiel. He endorses Thunberg’s motto – ‘Why learn, if there is no future?’ – with full conviction. “As a speaker at the German Fridays for Future he was already in one of the most famous talk shows in Germany”, says Van de Hulsbeek. “And he ended up in the office of the Minister of Economic Affairs, on the day that there was an important consultation on the closure of coal-fired power stations.”

On that day, thousands of students were in front of the Ministry in Berlin. They demand the fastest possible closure of the coal-fired power plants. …


Slightly more to the south, in Switzerland, tens of thousands of teenagers also skipped school for the climate. In December for the first time, the last two weeks again. …

The young people first demonstrated on Fridays and skipped their lessons. Last week they gathered on Saturday – so they could go to school the rest of the week.

United States

The Youth Climate Strike also includes students on the other side of the Atlantic Ocean. Take 13-year-old Alexandria Villasenor from New York. Inspired by young Thunberg she trudges every Friday to protest at the headquarters of the United Nations. She wants to organize a national strike with a group of environmental organizations on 15 March. “It is still unclear how many students want to participate and how the boards of those schools will respond,” says correspondent Wouter Zwart.

Demonstrating for a better climate is not new in the United States. Especially in the past two years the number of protests has increased. “It is a clear reaction to President Trump, who is rapidly reversing the climate measures that his predecessor Obama had introduced,” says Zwart. “The fact that America has withdrawn from the Paris Climate Agreement has caused bad blood among environmentally conscious young people.”

The rest of Europe

… In the United Kingdom a Youth Strike 4 Climate will be organized on 15 February. … “There were previous strikes by students, but that was rather small-scale.”

One of those students was 13-year-old Holly Gillibrand. The Scottish girl has been organizing her own ‘strike week’ for four weeks in a row. And in Dublin, hundreds of young people gathered in January at the Irish parliament building for the Children’s Rally for Climate Action.

In France, most students remained in school, but an online petition demanding action from the government on the climate has been signed more than 2.1 million times. In Italy it is mainly small groups of students who, inspired by the Swedish Thunberg, protest for a better climate.

The article mentions that in Thailand there is a call to protest as well.

Plant and fungi evolution, new study

This 2012 video says about itself:

Fungi: Death Becomes Them – CrashCourse Biology #39

Death is what fungi are all about. By feasting on the deceased remains of almost all organisms on the planet, converting the organic matter back into soil from which new life will spring, they perform perhaps the most vital function in the global food web. Fungi, which thrive on death, make all life possible.

From Virginia Tech in the USA:

A billion years of coexistence between plants and fungi

February 6, 2019

What can a billion years of coexistence tell us about the evolution of plants and fungi?

Neither plants nor fungi existed on land prior to 800 million years ago, an astonishing phenomenon considering their current immense biodiversity, ecosystem dominance, and impact on the environment.

Virginia Tech professor emeritus Khidir Hilu, along with a team of 13 researchers with complementary expertise in botany, mycology, paleontology, and bioinformatics, joined forces to address this question in a large-scale study published in Nature Communications.

“The movements of plants and fungi to land have irreversibly modified our planet physically and shaped their own biodiversity as well as that of the animal kingdom,” said Hilu, professor emeritus of the Department of Biological Sciences in the College of Science. “Our research shows that the successful plant and fungi invasion of land was an outcome of co-evolutionary interaction between the two that enhanced their biodiversities. These findings are timely considering current issues in climate change and notable extinctions experienced by plants and animals and the impact on our planet.”

The authors noted that although interactions between fungi and plants, including parasitism, mutualism (beneficial to both organisms), and saprotrophy (obtaining nutrients from dead plant parts), have been invoked as key mechanisms to their success, no one has explored contemporaneous evolutionary events throughout their history.

In this article, the authors methodologically explored the evolution of plants and fungi in a multiprong approach using molecular and bioinformatic techniques. They first established robust phylogenies, or evolutionary histories, for plants and fungi independently using gene sequence data generated in their labs or obtained from repositories of genome sequences.

Next, they estimated evolutionary divergence dates of plant and fungal lineages using both gene mutations and reliable fossil records. They then computed major shifts in diversification rates of major lineages in the two kingdoms independently. Once these studies were accomplished, the resulting phylogenetic relationships for plants and fungi were aligned on the same geological time scale, which allowed the researchers to pinpoint the origins of various key plant-fungal co-evolutionary events, particularly symbiotic relationships and the decomposition of plants by fungi. They noticed drastic shifts in diversification rates in the two kingdoms that convincingly showed plant-fungal co-evolution and interdependence across their long history.

The authors reported that fungal colonization of land was associated with and helped by at least two originations of terrestrial green algae, which preceded the origin of land plants. This coincided with the loss, ca. 720 million years ago, of fungal flagellum, a lash-like appendage that helps fungi swim in water.

Conversely, many million years later, during the Paleozoic Era, successful colonization of land by the lineage that eventually gave rise to all terrestrial plants living today was likely facilitated by fungi, specifically through fungal occupation of cells of the earliest land plants, promoting mutualism, which was key to plant and fungi success on land.

One of the significant biological, ecological, and environmental events on Earth is the origin and initial diversification of a lineage containing all plants that bear seeds. Seed plants, which include conifers and flowering plants, emerged during the Silurian Period about 436 million years ago. Significantly, one of the distinguishing traits of this plant lineage was the presence of a distinctive type of cell division that gave rise to wood. This led to the evolution of large woody trees, which in turn, resulted in the establishment of the first inland forests based on lignin-rich wood as their backbone.

Such a move could not have been successful without the linked evolution with fungi and their capacity to digest the structural polymer lignin and cellulose of plant cell walls. This evolutionary novelty was instrumental in organic matter recycling, which led to the forest system being sustained. The origin and early diversification of the seed plant lineage was in turn followed by the evolution of the largest classes of fungi, the Agaricomycetes.

The origin of ectomycorrhizal fungi (fungi associated externally with plant roots) seems to have resulted from a series of evolutionary innovations in plants including the origins of wood, seeds, and roots. These consequential evolutionary events were crucial in promoting the diversification leading to existing seed plants, including cone-bearing plants such as pines, spruces, maidenhairs, and cycads, as well as flowering plants, and their expansion to drier environments.

The latter group, in addition to including most living plant species and major ecosystems, such as forests and grasslands, also encompasses an astounding diversity in form and function and provides almost all of our food plants. Ectomycorrhizal fungi form a symbiotic relationship with plants and can produce networks around the plant roots to aid in water and nutrient uptake, often assisting the host plant to survive adverse weather conditions.

The macroevolution of plants and fungi has been studied mostly separately; however, this study clearly demonstrates that their respective evolutionary histories are deeply interconnected and can be understood only through a simultaneous study of their phylogenies within a robust timeframe.

It is expected that the same will hold true for the evolution of the animal kingdom, a group highly dependent on photoautotrophic plants, as well as microorganisms in general.

The symbiosis of plants and fungi has a great influence on the worldwide spread of plant species. In some cases, it even acts like a filter. This has been discovered by an international team of researchers with participation from the University of Göttingen. The results appeared in the journal Nature Ecology & Evolution: here.

Some fungi trade phosphorus with plants like savvy stockbrokers. New details show a fungus shifting its nutrient wares toward more favorable markets. By Susan Milius, 10:00am, June 10, 2019.

New York feeder birds

This video from New York state in the USA says about itself:

Cornell Feeders Turn Black And White – Feb. 6, 2019

Red-bellied and Downy Woodpeckers, Black-capped Chickadees, and White-breasted Nuthatches all wear feathers that are predominantly black, white, and gray. This color palette has us wondering if this is Casablanca or the Cornell Lab FeederWatch cam?

Watch LIVE at for news, updates, and more information about the pond and its surroundings.