Squid graveyard in Gulf of California

This video, from the Monterey Bay Aquarium Research Institute (MBARI) in the USA, says about itself:

Deep-Sea Discoveries: Squid Graveyard

15 March 2018

On an expedition in the Gulf of California, MBARI researchers discovered a surprising number of deep-sea squid carcasses on the ocean floor. The squid have a fascinating life history, but their story doesn’t end when they die. They become food for hungry scavengers and might change the rhythm of life in the deep sea.

Egg sheets were up to 2.5 m (over 8 feet) long.

The Gulf of California lies between mainland Mexico and Baja. MBARI researchers conducted expeditions there in 2003, 2012 and 2015.

For more information, see here.

Script and narration: Vicky Stein (MBARI Communications Intern)

Video producer: Linda Kuhnz

Music: Amazing Lake

Original journal article: Hoving, H.J.T., Bush, S.L., Haddock, S.H.D., Robison, B.H. (2017). Bathyal feasting: post-spawning squid as a source of carbon for deep-sea benthic communities. Proceedings of the Royal Society B. 284: 20172096.


Fruit flies like familiar songs

This 2017 video is called An introduction to Drosophila melanogaster.

From Nagoya University in Japan:

Even flies like a familiar song

How auditory learning shapes fly behavior

March 20, 2018

Summary: The process that allows sounds experienced during infancy to shape language is poorly understood. Researchers have found that courtship behavior in Drosophila melanogaster can be shaped by earlier auditory experiences. Their findings allowed them to develop a novel and simple neurological model to study how experiences of sound can shape complex modes of communication in animals.

The ability to learn and speak language depends heavily on the sounds and language we experience during early infancy. While this may sound self-evident, we still do not understand exactly what happens neurologically as a developing infant learns how to speak. In a study published in eLife, researchers at Nagoya University devised a new neurological model in fruit flies that may illuminate this process — and made some key discoveries about insect mating along the way.

“Higher mammalian species such as humans learn how to vocalize by listening to sounds from their own species”, lead author Xiaodong Li says. “Much of the research on how this occurs has been done in songbirds, which have much simpler neural circuits than humans. Even in songbirds, though, our understanding of how auditory inputs translate into vocalized outputs is still very rudimentary.”

To get around this intractable problem of complexity, the research team focused on Drosophila melanogaster. This unassuming fruit fly is commonly used in research as a model organism, because its biology is much simpler than humans — but surprisingly similar in fundamental ways. As fruit flies are unable to vocalize, however, the team studied a different mode of communication often shaped by auditory experience: courtship.

“As part of their courting ritual, male fruit flies vibrate their wings in pulses,” Li explains. “Every species of fruit fly is attracted to a unique wing pulse pattern. Attraction to a specific pulse is an evolutionary trait that promotes copulation while dissuading inter-species mating. Importantly, what we discovered was that this attraction is a learned behavior in fruit flies, contrary to the prevailing view that it happens innately.”

After emerging from their pupae as young adults, fruit flies spend a lot of time around their peers before they become mature enough to mate. The researchers hypothesized that exposure to these wing pulse “songs” during this time may teach them to prefer their species’ own pulse.

To test this idea, the team clipped the wings of young flies and put them in isolated chambers. The flies were either left alone to mature, or exposed to a sound that mimicked their species’ wing pulse. Males and females were then put together and another pulse was played, this time from a different species. If sexual preference was purely innate, the team reasoned, then the early exposure to their own species’ mating song would have no impact on the ‘dating’ that eventually commenced.

The result? When flies were first exposed to their own species’ song, subsequent mating went on in a typical fashion. Without the prior auditory training, however, the courtship ritual became notably less courtly: untrained females copulated in response to another species’ song, while untrained males began to chase one another (a behavior in the insect world known as “chaining”).

Though an intriguing discovery on its own, the researchers went one step further, seeking out the neurons responsible for this learned behavior. By experimentally manipulating levels of the neurotransmitter GABA and its receptor in the brain, the team pinpointed female pC1 neurons as crucial players in the courtship learning process. The discovery that fruit fly neurons can turn sound into sexual preference makes it possible to study how learning can shape communicative behaviors.

“The pC1 neuron cluster is known to be involved in evaluating sexual cues, but what we’ve found is that this cluster can be molded in response to auditory experiences during development,” lead investigator Azusa Kamikouchi says. “This finding opens up an entirely new research field. It allows us to use a highly tractable and simplified model in flies to study how auditory learning translates, at the neurological level, into sensorimotor behaviors that in many ways resemble the phenomenon of language.”

New fish species discovered near Caribbean Curaçao

This 20 March 2018 video is about the new fish species discovered in the new ocean zone called rariphotic.

From the Smithsonian Tropical Research Institute:

New deep reef ocean zone, the rariphotic, teeming with new fish species

New zone comprises reef fishes –including numerous new species — that live well below shallow coral reefs

March 20, 2018

Summary: Diving down below the range of scuba in the Curasub, Smithsonian deep reef explorers discovered a new world where roughly half of the fish had no names. They are calling it the rariphotic.

Based on the unique fish fauna observed from a manned submersible on a southern Caribbean reef system in Curaçao, Smithsonian explorers defined a new ocean-life zone, the rariphotic, between 130 and 309 meters (about 400 to 1,000 feet) below the surface. The rariphotic occurs just below a previously defined reef zone, the mesophotic, which extends from about 40 to as deep as 150 meters (about 120-450 feet). The role of this new zone as a refuge for shallower reef fishes seeking relief from warming surface waters or deteriorating coral reefs is still unclear.

The initial motivation for studying deep-reef ecosystems was the declining health of shallow reefs. Many researchers wonder if deeper reef areas, sometimes known as the “coral reef twilight zone”, might act as refuges for shallow-water organisms. As the Smithsonian researchers sought to answer this question, it became clear to them that scientists have only scratched the surface when it comes to understanding the biodiversity of reef fishes.

“It’s estimated that 95 percent of the livable space on our planet is in the ocean”, said Carole Baldwin, curator of fishes at the Smithsonian’s National Museum of Natural History, lead author of the study and director of the Smithsonian’s Deep Reef Observation Project (DROP). “Yet only a fraction of that space has been explored. That’s understandable for areas that are thousands of miles offshore and miles deep. But tropical deep reefs are just below popular, highly studied shallow reefs — essentially our own back yards. And tropical deep reefs are not barren landscapes on the deep ocean floor: they are highly diverse ecosystems that warrant further study. We hope that by naming the deep-reef rariphotic zone, we’ll draw attention to the need to continue to explore deep reefs.”

The authors defined the rariphotic based on depth observations of about 4,500 fishes representing 71 species during approximately 80 submersible dives to as deep as 309 meters. Most of the fishes in the rariphotic zone not only look similar to shallow reef fishes but are related to them rather than to true deep-ocean fishes, which belong to quite different branches of the evolutionary tree. This research showed that assemblages of the kinds of reef-fishes that inhabit shallow water in fact have double the depth range they were previously thought to have.

Since 2011, when DROP began, more than 40 researchers, most from the National Museum of Natural History and the Smithsonian Tropical Research Institute (STRI), have intensively studied deep-reef fishes and invertebrates off Curaçao. They named six new genera and about 30 new species as they explored a 0.2 square kilometer (0.08 square mile) area of reef, much of which is too deep for enough light to penetrate to support the algal symbionts on which reef-building corals rely.

“About one in every five fish we’re finding in the rariphotic of the Caribbean is a new species,” said D. Ross Robertson, marine biologist at STRI and a co-author of the study. “So far, my favorite is Haptoclinus dropi“. It was named by Baldwin and Robertson in 2013 for the Smithsonian’s DROP research project. Many more new species already discovered by DROP researchers await description.

While SCUBA divers can work down to about 40 meters (120 feet), the Curasub mini-submarine plunges to 309 meters (about 1,000 feet), where it can stay submerged for up to eight hours at normal atmospheric pressure, enabling the passengers to simply step ashore after a dive. This technology has significantly extended scientists’ ability to explore deep reefs.

Based on their research on reef fishes, the Smithsonian researchers and co-author Luke Tornabene (assistant professor at the University of Washington and former Smithsonian post-doctoral fellow) present a new classification of coral-reef faunal zones:

  • Altiphotic (high light): The new name for the previously unnamed 0-40 meters (0-120 feet), the well-lit zone where reef corals are abundant, which extends as deep as conventional scuba divers normally go.
  • Mesophotic (medium light): 40 to as deep as 150 meters (120-450 feet), the maximum depth at which tropical reef-building corals and their algal symbionts can survive.
  • Rariphotic (low light): Newly discovered faunal zone from 130-300 meters (400-1,000 feet), below the reef-building coral zone, and as deep as Curasub can go.
  • Deep aphotic (effectively no light): Below 300 meters (below 1,000 feet)

“Reef ecosystems just below the mesophotic are globally underexplored, and the conventional view based on the few studies that mention them was that mesophotic ecosystems transition directly into those of the deep sea“, Baldwin said. “Our study reveals a previously unrecognized zone comprising reef vs. deep-sea fishes that links mesophotic and deep-sea ecosystems.”

Blue jay migration in North America

This video from North America says about itself:

19 March 2018

The blue jay migration is a hard one to figure out. Some birds migrate and some don’t.

How termites recognize queens, kings

This 2009 video says about itself:

Her Majesty, The Termite Queen | National Geographic

Journey to the center of the…termite nest? Hard to believe this termite queen will produce almost 165 million eggs in her lifetime!

From North Carolina State University in the USA:

Termite queen, king recognition pheromone identified

March 19, 2018

Summary: Forget the bows and curtsies. Worker termites shake in the presence of their queens and kings. New research explains how these workers smell a royal presence.

Researchers at North Carolina State University have for the first time identified a specific chemical used by the higher termite castes — the queens and the kings — to communicate their royal status with worker termites. The findings could advance knowledge of termite evolution, behavior and control.

A study published in Proceedings of the National Academy of Sciences shows that a wax-like hydrocarbon — a chemical consisting of only carbon and hydrogen atoms called heneicosane — on the body surface of subterranean royal termites is used to enable worker termites to recognize and care for them. Termites live mostly underground or in wood and are generally blind, necessitating the use of chemical signals to communicate.

“This is the first report of a queen recognition pheromone in termites and the first report of a king recognition pheromone in insects”, said Coby Schal, Blanton J. Whitmire Distinguished Professor of Entomology at NC State.

Schal and NC State Ph.D. graduate Colin Funaro, the paper’s co-corresponding authors, used gas chromatography to isolate specific chemicals from the exoskeletons of royal and worker Reticulitermes flavipes termites and found heneicosane on the royal termites, but not on workers.

When heneicosane was placed on glass dummies serving as royal termite proxies, workers did not bow or curtsy, but instead started shaking — an action that seemed to reflect the termite version of royal recognition. Workers shook even more when the royal pheromone was blended with other hydrocarbons from the colony’s workers that represent the colony’s odor.

“Termites use a two-step recognition process — the colony’s odor gives workers a ‘home’ context and heneicosane within this context denotes ‘royals are in the home'”, Schal said.

“The royal-recognition pheromone lets workers know that there is a queen or a king present and that everything is stable in the colony”, Funaro said. “Worker termites shook more when realizing that the royals were also nest mates.”

Schal said that the study upends the commonly held belief that queens of the insect order Hymenoptera — ants, bees and wasps — were the first to use these wax-like hydrocarbon pheromones for royal recognition.

“Termites appeared some 150 million years ago while the social Hymenoptera appeared about 100 million years ago, so this discovery of a hydrocarbon as a royal-recognition pheromone in termites appears to predate its use in [other] social insects“, Schal said.

R. flavipes termites are major pests in North Carolina and the Southeast, causing billions in damage, Schal added. In recent years they have spread to the west coast of the U.S., and into Canada, South America, Europe, and Asia.

Jumbo squid video

This BBC video says about itself:

Jumbo squid caught on camera for Blue Planet II | Earth Unplugged

8 March 2018

Profile on Edith Widder, bioluminescence expert who took enormous steps in understanding animals’ behaviour in the deep sea.

Hispaniolan solenodon DNA sequenced

This video says about itself:

4 May 2016

Researchers from the University of Illinois and the University of Puerto Rico sequenced the DNA of Hispaniolan solenodons, revealing the mammal to be approximately 78 million years old.

From GigaScience:

Menomous [sic; Venomous] Solenodon, last survivor of a branch of mammals that appeared at the time of the dinosaurs, sequenced

March 16, 2018

Summary: An article presents a draft genome of a small shrew-like animal, the venomous Hispaniolan solenodon. This unusual animal is one of the only extant venomous mammals, and it is the sole remaining branch of mammals that split from other insectivores at the time of the dinosaurs. The solenodon genome sequence revealed the answer to several evolutionary questions, such as whether the solenodon species indeed survived the meteor impact that killed the dinosaurs.

Published today, in the open-access journal GigaScience, is an article that presents a draft genome of a small shrew-like animal, the venomous Hispaniolan solenodon (Solenodon paradoxus). This species is unusual not only because it is one of the very few venomous mammals, it is also the sole remaining branch of mammals that split from other insectivores at the time of the dinosaurs. The genome sequencing and analysis of this endangered animal was carried out by an international team lead by Dr. Taras K. Oleksyk from the University of Puerto Rico at Mayagüez. The availability of the solenodon genome sequence allowed the researchers to answer several evolutionary questions, particularly whether the solenodon species indeed survived the meteor impact that laid waste to the dinosaurs.

As one of the only extant mammals that are venomous, the Solenodon’s venomous saliva flows from modified salivary glands through grooves on their sharp incisors (“solenodon” derives from the Greek for “grooved tooth”). They also have several other primitive and very unusual characteristics for a mammal: very large claws, a flexible snout with a ball-and-socket joint, and oddly positioned teats, which are on their rear. While the mammalian tree of life has been heavily researched, this is the most distantly related branch to be added to the ‘genome club’. It has particular importance and implications for conservation because morphometric studies have suggested that southern and northern Hispaniolan solenodons may be subspecies rather than separate species.

Solenodon is not just genetically but also geographically isolated. Highly endangered, they remain only in a few remote corners of the Caribbean islands of Cuba and Hispaniola. Its nocturnal lifestyle makes it even more elusive and therefore less studied. Thus, it was crucial for the researchers to work with local experts at the Instituto Tecnológico de Santo Domingo and Universidad Autónoma de Santo Domingo and with local guides who helped them track and ambush passing solenodons at night.

One of the lead authors, Dr Juan Carlos Martinez-Cruzado, noted that “local resources are absolutely necessary for this kind of work; only they truly know their animal’s behavior.” He added, “this project may open doors to many others to come, and we always assumed this to be one of many projects that will help research, education and conservation efforts in the Dominican Republic.”

For this project, there was more than just the challenge of obtaining the organisms for blood samples, the solenodon genome proved particularly difficult to sequence. Carrying out genomics research in remote parts of the Caribbean provided a challenge, particularly in transporting high quality DNA to the lab. Due to the constraints of poor quality DNA as well as a limited budget, the commercial lab used to carry out the sequencing turned out a very low coverage per individual.

Having already ventured into the jungle, the researchers embraced this new challenge by coming up with novel approaches to assemble the genome. First, the researchers reasoned that because the species has existed for tens of millions of years in isolation, it was extremely inbred and had a very homozygous genome. This lead to a potential work-around, because the five collected sets of genomic data could be pooled to increase the coverage. Despite initial doubts, this worked better than expected especially when that strategy was combined with using a string graph approach rather than the more standard de Brujn graph assembly method. String graphs incorporate more of the sequencing data than de Brujn graphs. Based on the results here, this new technique provides a low budget alternative for genome assembly, particularly in the highly homozygous genomes of endangered species.

The first author of the paper, Kirill Grigorev elaborates: “For me, perhaps the most interesting part of this research was the challenge of delivering a de novo genome assembly that was suitable for comparative genomics, using an amount of sequencing data much smaller than in other similar projects.”

After carrying out their assembly, the researchers had data of sufficient quality for answering many scientific questions on solenodon evolution. With regard to conservation plans, the data supports that there was a subspecies split within the Hispaniolan solenodon at least 300,000 years ago, meaning the northern and southern populations should be treated as two separate conservation units and may therefore need independent breeding strategies.

These data also shed light on the initial speciation event for this branch, and showed that solenodons likely diverged from other extant mammals 73.6 million years ago. Dr. Oleksyk said: “We have confirmed the early speciation date for Solenodons, weighing on the ongoing debate on whether the solenodons have indeed survived the demise of dinosaurs after the asteroid impact in the Caribbean.”

This research was the inaugural winner of the GigaScience prize at the International Conference on Genomics in Shenzhen on the 30st October 2017. Presenting in the prize track, the international panel of judges voted the paper the winner of the $1000 prize and trophy. The GigaScience prize track will run again at ICG-13, and the journal will begin taking papers for it next month. Follow GigaScience on social media for more information.