Giant squid genome research


This 2015 video says about itself:

A giant Architeuthis dux squid was caught on camera when it swam into a harbor in Japan on Christmas Eve. The young squid is estimated to be 12 feet long, and scientists say the species can reach over 40 feet in length.

From the Marine Biological Laboratory in the USA:

The mysterious, legendary giant squid’s genome is revealed

January 16, 2020

How did the monstrous giant squid — reaching school-bus size, with eyes as big as dinner plates and tentacles that can snatch prey 10 yards away — get so scarily big?

Today, important clues about the anatomy and evolution of the mysterious giant squid (Architeuthis dux) are revealed through publication of its full genome sequence by a University of Copenhagen-led team that includes scientist Caroline Albertin of the Marine Biological Laboratory (MBL), Woods Hole.

Giant squid are rarely sighted and have never been caught and kept alive, meaning their biology (even how they reproduce) is still largely a mystery. The genome sequence can provide important insight.

“In terms of their genes, we found the giant squid look a lot like other animals. This means we can study these truly bizarre animals to learn more about ourselves,” says Albertin, who in 2015 led the team that sequenced the first genome of a cephalopod (the group that includes squid, octopus, cuttlefish, and nautilus).

Led by Rute da Fonseca at University of Copenhagen, the team discovered that the giant squid genome is big: with an estimated 2.7 billion DNA base pairs, it’s about 90 percent the size of the human genome.

Albertin analyzed several ancient, well-known gene families in the giant squid, drawing comparisons with the four other cephalopod species that have been sequenced and with the human genome.

She found that important developmental genes in almost all animals (Hox and Wnt) were present in single copies only in the giant squid genome. That means this gigantic, invertebrate creature — long a source of sea-monster lore — did NOT get so big through whole-genome duplication, a strategy that evolution took long ago to increase the size of vertebrates.

So, knowing how this squid species got so giant awaits further probing of its genome.

“A genome is a first step for answering a lot of questions about the biology of these very weird animals,” Albertin said, such as how they acquired the largest brain among the invertebrates, their sophisticated behaviors and agility, and their incredible skill at instantaneous camouflage.

“While cephalopods have many complex and elaborate features, they are thought to have evolved independently of the vertebrates. By comparing their genomes we can ask, ‘Are cephalopods and vertebrates built the same way or are they built differently?'” Albertin says.

Albertin also identified more than 100 genes in the protocadherin family — typically not found in abundance in invertebrates — in the giant squid genome.

“Protocadherins are thought to be important in wiring up a complicated brain correctly,” she says. “They were thought they were a vertebrate innovation, so we were really surprised when we found more than 100 of them in the octopus genome (in 2015). That seemed like a smoking gun to how you make a complicated brain. And we have found a similar expansion of protocadherins in the giant squid, as well.”

Lastly, she analyzed a gene family that (so far) is unique to cephalopods, called reflectins. “Reflectins encode a protein that is involved in making iridescence. Color is an important part of camouflage, so we are trying to understand what this gene family is doing and how it works,” Albertin says.

“Having this giant squid genome is an important node in helping us understand what makes a cephalopod a cephalopod. And it also can help us understand how new and novel genes arise in evolution and development.”

Damselfly, dragonfly evolution, new resesarch


This 2014 video is called The Secret World of Dragonflies.

From the University of Minnesota in the USA:

Glimpse into ancient hunting strategies of dragonflies and damselflies

January 16, 2020

Dragonflies and damselflies are animals that may appear gentle but are, in fact, ancient hunters. The closely related insects shared an ancestor over 250 million years ago — long before dinosaurs — and provide a glimpse into how an ancient neural system controlled precise and swift aerial assaults.

A paper recently published in Current Biology, led by University of Minnesota researchers, shows that despite the distinct hunting strategies of dragonflies and damselflies, the two groups share key neurons in the circuit that drives the hunting flight. These neurons are so similar, researchers believe the insects inherited them from their shared ancestor and that the neurons haven’t changed much.

Gaining insight into their ability to quickly process images could inform technological advancements. These findings could inform where to mount cameras on drones and autonomous vehicles, and how to process the incoming information quickly and efficiently.

“Dragonflies and damselflies are interesting from an evolutionary point of view because they give us a window into ancient neural systems,” said Paloma Gonzalez-Bellido, assistant professor in the Department of Ecology, Evolution and Behavior in the College of Biological Sciences and senior author on the paper. “And because there are so many species, we can study their behavior and compare their neural performance. You can’t get that from fossils.”

A noticeable difference between dragonflies and damselflies is the shape and position of their eyes. Most dragonflies today have eyes that are close together, often touching along the top of their head. Whereas damselflies sport eyes that are far apart. The researchers wanted to know whether this made a difference in their hunting habits, and if it affected how their neural system detects moving prey.

Researchers found:

  • dragonflies and damselflies hunt prey differently, with dragonflies using a higher resolution area near the top of their eyes to hunt prey from below and damselflies leveraging increased resolution in the front of their eyes to hunt prey in front of them;
  • in dragonflies with eyes that merge at the top, the eyes work as if they were two screens of an extended display (i.e. the image of the prey, which would be equivalent to the mouse pointer, can fall on either the left or the right, but never in both screens at the same time);
  • damselflies eyes work as duplicated screens, where the prey image is seen by both eyes at once (i.e. they have binocular vision);
  • both designs have pros and cons, and their presence correlates with the type of prey and the environment;
  • despite different strategies, the neurons that transfer information about a moving target from the brain to the wing motor centers are nearly identical in the two groups — indicating they were inherited from the common ancestor.

The different hunting strategies pay off in different environments. Dragonflies tend to hunt in an open area, leveraging the contrast of the sky to help them spot their target. Although they can’t calculate depth using two images, they rely on other cues. Damselflies tend to hunt among vegetation, where the selective pressure for fast reaction may be absent, or the need for depth perception stronger.

Researchers are now looking to understand how the extended versus duplicated images are calculated in the brain, and how the information is implemented into muscle movements.

“There is still a lot we do not understand,” said Jack Supple, first author and a recent PhD graduate from Gonzalez-Bellidos laboratory. “We do not know how these neurons coordinate all the different muscles in the body during flight. If we tried to build a realistic robotic damselfly or dragonfly tomorrow we would have a difficult time.”

In addition to examining the differences amongst the two insect families, researchers continue to explore differences in species within each family. “While most dragonflies have eyes close together, there are a handful of species with eyes far apart,” said Gonzalez-Bellido. “Some of them are abundant in Minnesota and we are eager to leverage the new flight arena to study their behavior in a controlled setting.”

Researchers aim to collect at Cedar Creek Ecosystem Science Reserve and Itasca Biological Station and Laboratories this summer, both areas with diverse populations of dragonflies and damselflies.

Ancient scorpion, oldest land animal?


The fossil (left) was unearthed in Wisconsin in 1985. Scientists analyzed it and discovered the ancient animal's respiratory and circulatory organs (center) were near-identical to those of a modern-day scorpion (right). Images courtesy Andrew Wendruff

From Ohio State University in the USA:

Fossil is the oldest-known scorpion

Researchers think it was one of the first animals to spend time on land

January 16, 2020

Scientists studying fossils collected 35 years ago have identified them as the oldest-known scorpion species, a prehistoric animal from about 437 million years ago. The researchers found that the animal likely had the capacity to breathe in both ancient oceans and on land.

The discovery provides new information about how animals transitioned from living in the sea to living entirely on land: The scorpion‘s respiratory and circulatory systems are almost identical to those of our modern-day scorpions — which spend their lives exclusively on land — and operate similarly to those of a horseshoe crab, which lives mostly in the water, but which is capable of forays onto land for short periods of time.

The researchers named the new scorpion Parioscorpio venator. The genus name means “progenitor scorpion,” and the species name means “hunter.” They outlined their findings in a study published today in the journal Scientific Reports.

“We’re looking at the oldest known scorpion — the oldest known member of the arachnid lineage, which has been one of the most successful land-going creatures in all of Earth history,” said Loren Babcock, an author of the study and a professor of earth sciences at The Ohio State University.

“And beyond that, what is of even greater significance is that we’ve identified a mechanism by which animals made that critical transition from a marine habitat to a terrestrial habitat. It provides a model for other kinds of animals that have made that transition including, potentially, vertebrate animals. It’s a groundbreaking discovery.”

The “hunter scorpion” fossils were unearthed in 1985 from a site in Wisconsin that was once a small pool at the base of an island cliff face. They had remained unstudied in a museum at the University of Wisconsin for more than 30 years when one of Babcock’s doctoral students, Andrew Wendruff — now an adjunct professor at Otterbein University in Westerville — decided to examine the fossils in detail.

Wendruff and Babcock knew almost immediately that the fossils were scorpions. But, initially, they were not sure how close these fossils were to the roots of arachnid evolutionary history. The earliest known scorpion to that point had been found in Scotland and dated to about 434 million years ago. Scorpions, paleontologists knew, were one of the first animals to live on land full-time.

The Wisconsin fossils, the researchers ultimately determined, are between 1 million and 3 million years older than the fossil from Scotland. They figured out how old this scorpion was from other fossils in the same formation. Those fossils came from creatures that scientists think lived between 436.5 and 437.5 million years ago, during the early part of the Silurian period, the third period in the Paleozoic era.

“People often think we use carbon dating to determine the age of fossils, but that doesn’t work for something this old,” Wendruff said. “But we date things with ash beds — and when we don’t have volcanic ash beds, we use these microfossils and correlate the years when those creatures were on Earth. It’s a little bit of comparative dating.”

The Wisconsin fossils — from a formation that contains fossils known as the Waukesha Biota — show features typical of a scorpion, but detailed analysis showed some characteristics that were not previously known in any scorpion, such as additional body segments and a short “tail” region, all of which shed light on the ancestry of this group.

Wendruff examined the fossils under a microscope, and took detailed, high-resolution photographs of the fossils from different angles. Bits of the animal’s internal organs, preserved in the rock, began to emerge. He identified the appendages, a chamber where the animal would have stored its venom, and — most importantly — the remains of its respiratory and circulatory systems.

This scorpion is about 2.5 centimeters long — about the same size as many scorpions in the world today. And, Babcock said, it shows a crucial evolutionary link between the way ancient ancestors of scorpions respired under water, and the way modern-day scorpions breathe on land. Internally, the respiratory-circulatory system has a structure just like that found in today’s scorpions.

“The inner workings of the respiratory-circulatory system in this animal are, shape-wise, identical to those of the arachnids and scorpions that breathe air exclusively,” Babcock said. “But it also is incredibly similar to what we recognize in marine arthropods like horseshoe crabs. So, it looks like this scorpion, this lineage, must have been pre-adapted to life on land, meaning they had the morphologic capability to make that transition, even before they first stepped onto land.”

Paleontologists have for years debated how animals moved from sea to land. Some fossils show walking traces in the sand that may be as old as 560 million years, but these traces may have been made in prehistoric surf — meaning it is difficult to know whether animals were living on land or darting out from their homes in the ancient ocean.

But with these prehistoric scorpions, Wendruff said, there was little doubt that they could survive on land because of the similarities to modern-day scorpions in the respiratory and circulatory systems.

Neanderthals used seashells as tools, new research


This October 2014 video is called A Neanderthal Perspective on Human Origins.

From PLOS:

Neanderthals went underwater for their tools

Neanderthals collected clamshells and pumice from coastal waters to use as tools

January 15, 2020

Neanderthals collected clamshells and volcanic rock from the beach and coastal waters of Italy during the Middle Paleolithic, according to a study published January 15, 2020 in the open-access journal PLOS ONE by Paola Villa of the University of Colorado and colleagues.

Neanderthals are known to have used tools, but the extent to which they were able to exploit coastal resources has been questioned. In this study, Villa and colleagues explored artifacts from the Neanderthal archaeological cave site of Grotta dei Moscerini in Italy, one of two Neanderthal sites in the country with an abundance of hand-modified clamshells, dating back to around 100,000 years ago.

The authors examined 171 modified shells, most of which had been retouched to be used as scrapers. All of these shells belonged to the Mediterranean smooth clam species Callista chione. Based on the state of preservation of the shells, including shell damage and encrustation on the shells by marine organisms, the authors inferred that nearly a quarter of the shells had been collected underwater from the seafloor, as live animals, as opposed to being washed up on the beach. In the same cave sediments, the authors also found abundant pumice stones likely used as abrading tools, which apparently drifted via sea currents from erupting volcanoes in the Gulf of Naples (70km south) onto the Moscerini beach, where they were collected by Neanderthals.

These findings join a growing list of evidence that Neanderthals in Western Europe were in the practice of wading or diving into coastal waters to collect resources long before Homo sapiens brought these habits to the region. The authors also note that shell tools were abundant in sediment layers that had few stone tools, suggesting Neanderthals might have turned to making shell tools during times where more typical stone materials were scarce (though it’s also possible that clam shells were used because they have a thin and sharp cutting edge, which can be maintained through re-sharpening, unlike flint tools).

The authors add: “The cave opens on a beach. It has a large assemblage of 171 tools made on shells collected on the beach or gathered directly from the seafloor as live animals by skin diving Neanderthals. Skin diving for shells or freshwater fishing in low waters was a common activity of Neanderthals, according to data from other sites and from an anatomical study published by E. Trinkaus. Neanderthals also collected pumices erupted from volcanoes in the Gulf of Naples and transported by sea to the beach.”

Queen scallops near Terschelling island


This 17 March 2018 video says about itself:

Queen Scallop, Aequipecten opercularis, in natural sandy seabed, Bovisand, Plymouth, England. Filmed in time-lapse they have been placed in front of the camera but soon decide to leave – pumping themselves up as if ready to suddenly jet off. Various periwinkle snails can be seen burying themselves in the sand. Queen scallops are edible and part of a big fishery off the Isle of Man.

On 15 December 2020, warden Joeri Lamers reported that many queen scallops had beached on Terschelling island. So many that he suspects they now live not far from Terschelling, where they were unknown as a resident species before.

Not even water bears survive global warming


This December 2018 video says about itself:

Tardigrades are the most resilient animals in the universe, and there’s probably one within a stone’s throw from you right now.

From the Faculty of Science – University of Copenhagen in Denmark:

High temperatures due to global warming will be dramatic even for tardigrades

January 13, 2020

Summary: A research group has just shown that tardigrades are very vulnerable to long-term high temperature exposures. The tiny animals, in their desiccated state, are best known for their extraordinary tolerance to extreme environments.

Global warming, a major aspect of climate change, is already causing a wide range of negative impacts on many habitats of our planet. It is thus of the utmost importance to understand how rising temperatures may affect animal health and welfare.

A research group from Department of Biology, University of Copenhagen has just shown that tardigrades are very vulnerable to long-term high temperature exposures. The tiny animals, in their desiccated state, are best known for their extraordinary tolerance to extreme environments.

In a study published recently in Scientific Reports, Ricardo Neves and Nadja Møbjerg and colleagues at Department of Biology, University of Copenhagen present results on the tolerance to high temperatures of a tardigrade species.

Tardigrades, commonly known as water bears or moss piglets, are microscopic invertebrates distributed worldwide in marine, freshwater and terrestrial microhabitats.

Ricardo Neves, Nadja Møbjerg and colleagues investigated the tolerance to high temperatures of Ramazzottius varieornatus, a tardigrade frequently found in transient freshwater habitats.

“The specimens used in this study were obtained from roof gutters of a house located in Nivå, Denmark. We evaluated the effect of exposures to high temperature in active and desiccated tardigrades, and we also investigated the effect of a brief acclimation period on active animals,” explains postdoc Ricardo Neves.

Rather surprisingly the researchers estimated that for non-acclimated active tardigrades the median lethal temperature is 37.1°C, though a short acclimation periods leads to a small but significant increase of the median lethal temperature to 37.6°C. Interestingly, this temperature is not far from the currently measured maximum temperature in Denmark, i.e. 36.4°C. As for the desiccated specimens, the authors observed that the estimated 50% mortality temperature is 82.7°C following 1 hour exposures, though a significant decrease to 63.1°C following 24 hour exposures was registered.

The research group used logistic models to estimate the median lethal temperature (at which 50% mortality is achieved) both for active and desiccated tardigrades.

Approximately 1300 tardigrade species have been described so far. The body of these minute animals is barrel-shaped (or dorsoventrally compressed) and divided into a head and a trunk with four pairs of legs. Their body length varies between 50 micrometers and 1.2 millimeters. Apart from their impressive ability to tolerate extreme environments, tardigrades are also very interesting because of their close evolutionary relationship with arthropods (e.g., insects, crustaceans, spiders).

As aquatic animals, tardigrades need to be surrounded in a film of water to be in their active state (i.e., feeding and reproducing). However, these critters are able to endure periods of desiccation (anhydrobiosis) by entering cryptobiosis, i.e., a reversible ametabolic state common especially among limno-terrestrial species. Succinctly, tardigrades enter the so-called “tun” state by contracting their anterior-posterior body axis, retracting their legs and rearranging the internal organs. This provides them with the capacity to tolerate severe environmental conditions including oxygen depletion (anoxybiosis), high toxicant concentrations (chemobiosis), high solute concentration (osmobiosis) and extremely low temperatures (cryobiosis).

The extraordinary tolerance of tardigrades to extreme environments includes also high temperature endurance. Some tardigrade species were reported to tolerate temperatures as high as 151°C. However, the exposure time was only of 30 minutes. Other studies on thermotolerance of desiccated (anhydrobiotic) tardigrades revealed that exposures higher than 80°C for 1 hour resulted in high mortality, with almost all specimens dying at temperatures above 103°C. It remained, yet, unknown how anhydrobiotic tardigrades handle exposures to high temperatures for long periods, i.e., exceeding 1 hour.

“From this study, we can conclude that active tardigrades are vulnerable to high temperatures, though it seems that these critters would be able to acclimatize to increasing temperatures in their natural habitat. Desiccated tardigrades are much more resilient and can endure temperatures much higher than those endured by active tardigrades. However, exposure-time is clearly a limiting factor that constrains their tolerance to high temperatures,” says Ricardo Neves.

Indeed, although tardigrades are able to tolerate a diverse set of severe environmental conditions, their endurance to high temperatures is noticeably limited and this might actually be the Achilles heel of these otherwise super-resistant animals.

Fifteen new South American wasp species discovered


This 2009 video says about itself:

A parasitic wasp has injected her eggs into a caterpillar — and now they’re ready to hatch.

From the University of Turku in Finland:

New parasitoid wasp species discovered in the Amazon — can manipulate host’s behavior

January 14, 2020

A research group from the Biodiversity Unit of the University of Turku studies the diversity of parasitoid insects around the world. Parasitoid wasps (Hymenoptera) are one of the most species-rich animal taxa on Earth, but their tropical diversity is still poorly known. In the latest study, the group discovered 15 new, sizeable species that parasitise spiders in the lowland rainforests of the Amazon and the cloud forests of the Andes.

The researchers from the Biodiversity Unit of the University of Turku have studied the diversity of tropical parasitoid insects for almost 20 years already. During their research, they have discovered large numbers of new species from different parts of the world. In the newest study, the research group sampled parasitoid wasps of the genus Acrotaphus, which parasitise spiders. The diversity of the insects was studied in e.g. the tropical Andes and the lowland rainforest areas of the Amazon. The research was conducted in cooperation with the Brazilian INPA (Instituto Nacional de Pesquisas da Amazônia) research unit.

Acrotaphus wasps are fascinating because they are very sizeable parasitoids. The largest species can grow multiple centimetres in length and are also very colourful. Previously, only 11 species of the genus were known, so this new research gives significant new information on the diversity of insects in rain forests, tells postdoctoral researcher and lead author of the new study Diego Pádua, who has worked both for the INPA and the Biodiversity Unit of the University of Turku.

The parasitoid Acrotaphus wasps parasitise on spiders. A female Acrotaphus attacks a spider in its web and temporarily paralyses it with a venomous sting. After this, the wasp lays a single egg on the spider, and a larva hatches from the egg. The larva gradually consumes the spider and eventually pupates.

The Acrotaphus wasps we studied are very interesting as they are able to manipulate the behaviour of the host spider in a complex way. During the time period preceding the host spider’s death, it does not spin a normal web for catching prey. Instead, the parasitoid wasp manipulates it into spinning a special web which protects the developing pupa from predators. Host manipulation is a rare phenomenon in nature, which makes these parasitoid wasps very exciting in terms of their evolution, tells Ilari E. Sääksjärvi, Professor of Biodiversity research from the University of Turku.

The University of Turku and INPA continue to study the diversity of the parasitoid wasps in collaboration in the west Amazon area and in the Andes. On each research trip, the researchers discover many new species with unknown habits.