Meet your distant relative, Entelognathus primordialis, possibly the first earthling with a face. Or at least a familiar face.

Entelognathus primordialis (where Entelognathus means “complete jaw”) is described this week in Nature. Discovered in a quarry in China, the remarkably well-preserved fossil is somewhat 3D, displaying a modern type of jaw.

E. primordialis is a placoderm, an early class of fish that lived 430 to 360 million years ago. These fish were covered with an armor of bony plates and gave rise to two later groups—bony fish and cartilaginous fish.

The evolution of jaws is one of the key episodes in the evolution of vertebrates, but the gap between jawed and jawless vertebrates is so large that it has been hard to work out the individual evolutionary steps in the transition. Min Zhu and his colleagues hope to make the link with E. primordialis.

The 419 million-year-old fish fossil has jawbone features previously restricted to bony fishes, but has the full body armor seen in placoderms. It would have been around 20 centimeters (eight inches) long.

Prior to this recent find, most scientists agreed that placoderms had no jaw and were more similar to the cartilaginous fish, like modern day sharks, while the bony fishes are believed to be our ancestors. According to Nature News:

Such fishes went on to dominate the seas and ultimately gave rise to land vertebrates.

In addition to facing off with placoderms, the new study puts cartilaginous fishes into a whole new light—perhaps they are even more evolved than previously thought.

Can scientists pull off a real-life version of Jurassic Park?  This intriguing question received a lot of attention earlier this year, when Revive & Restore (a project of the San Francisco-based Long Now Foundation) announced their goal of reviving extinct species using cutting-edge DNA technology. Dinosaurs have been gone too long for DNA to still be intact, but animals that went extinct during human history could potentially make a comeback. One of the first candidates for “de-extinction”—the iconic passenger pigeon (Ectopistes migratorius).

In the early 1800s, the passenger pigeon was the world’s most abundant bird species, even though its range was limited to eastern and central North America. Flocks of passenger pigeons—which sometimes included millions of birds—were so vast, they darkened swaths of sky up to a mile wide. But intensive hunting and habitat destruction by humans drove this species to extinction in a shockingly short span of time. The last passenger pigeon, “Martha,” died in 1914 at the Cincinnati Zoo. Her body remains at the Smithsonian’s National Museum of Natural History.

The Academy’s research collection houses nine specimens and three eggs of this species, dating to the late 1800s. Century-old specimens like these can still provide valuable information for modern-day studies. For example, Academy curator Jack Dumbacher and his colleagues published a paper in 2010 revealing that the closest living relative of the passenger pigeon is not the mourning dove, as many had suspected, but the band-tailed pigeon (Patagioenas fasciata), which is found along the Pacific coast and in the southwestern U.S., and can be seen in oak forests in the Bay Area. DNA sampling from museum specimens provided crucial data for this study. And the study’s conclusion provides critical information about which living relative could serve as a surrogate parent for the passenger pigeon, as scientists move forward with trying to revive this lost species.

Science Today sat down with Jack Dumbacher, who is also a scientific advisor to the Long Now Foundation, for his insights into de-extinction.

Where does the process currently stand?
JD: The Long Now Foundation has assembled a team of scientists to tackle different aspects of this project. Graduate student Ben Novak, working in Beth Shapiro’s lab at UC Santa Cruz, is refining the sequencing of the passenger pigeon genome from museum specimens. The genome of the band-tailed pigeon (the closest living relative) is also being sequenced.

Once the genomes are assembled, what happens next?
JD: You have to compare the genomes to determine which stretches of DNA make a passenger pigeon a passenger pigeon. Then you take the genome of a band-tailed pigeon and convert those important stretches of DNA into passenger pigeon DNA. George Church’s lab at Harvard is working on ways to do this using “CRISPR” technology—using bacterial proteins to genetically engineer specific DNA sequences and direct mutations to occur in a predictable way.

Let’s say scientists successfully get this DNA into an embryo, and the embryo becomes a chick. Is it a true passenger pigeon?
JD: That’s the big challenge. It may still have some band-tailed pigeon DNA. And you have to think about its behavior. How will it learn to be a passenger pigeon, find food, and avoid predators? Teams of researchers are tackling these numerous considerations and challenges.

Some might say that extinct animals went extinct for a reason, and bringing them back is not a good idea. How would you respond
JD: Animals like the passenger pigeon and moa went extinct due to human activity. So going extinct “for a reason” was humans to begin with. Also, developing the technology to successfully de-extinct an animal would itself be an intellectual coup, one that might have unforeseen benefits. The technology could be useful in other aspects of life, like agriculture, animal husbandry, conservation of endangered species, and, potentially, even human health. Think of the Space Race and all the accompanying benefits to society that resulted from that fundamental scientific research and development.

What other ethical concerns have come up?
JD: The ideal goal is to release de-extincted passenger pigeons back into their native habitat. But you have to be careful not to harm any other species whose survival may be on the brink. Their original ecosystem (the forests of the eastern and central U.S.) has changed. You don’t want to upset the balance in a way that threatens additional species. But the idea of restoring a habitat with native species is not a new one. Biologists restore habitats all the time. Had the pigeon survived only in captivity, we would be excited to be able to re-release it. Having survived only in our freezers or museum drawers, is that so different?

How many years away are we from seeing a real, live passenger pigeon?
JD: Optimistically, I would be very excited if this could happen in the next five to ten years. If not, I am confident that some day, we will have the technology to do this. Now is a good time to start thinking critically about what such a technology and ability would mean.

Andrew Ng is Communications Manager at the California Academy of Sciences.

It’s sea otter awareness week, which seems like a great time to reveal something heroic about this charismatic animal. A recent study from UC Santa Cruz concluded that sea otters are helping to save the ocean—with their appetites.

When you think of sea otters, you may think “cute and cuddly,” but these playful marine mammals are top predators, like great white sharks and tigers, and their hunt for food is helping to maintain ecosystem health along portions of California’s coastline.

The sea otter’s role in ecosystem management begins with one of its preferred foods: crabs. Sea otters eat crabs. Crabs in turn eat sea slugs and small crustaceans. The slugs and crustaceans eat algae off sea plants, keeping them green and healthy. It’s a relatively typical food web but now it’s clear: The healthier the crab-eating otter population is, the healthier the plants tend to be.

Sea plants, like eelgrass, along the west coast are important habitat for fish such as Pacific herring, halibut and salmon. They also protect shorelines from storms and waves, and they soak up carbon dioxide from seawater and the atmosphere.  Thus, a healthy coastal ecosystem has the right mix of otters eating crabs and invertebrates eating algae.

Unfortunately, seagrass meadows have been declining worldwide, partly due to excessive nutrients from agricultural and urban runoff entering coastal waters.  When sewage and agricultural waste like fertilizers spill into the sea, ecosystems suffer. Excessive nitrogen and phosphorus in the water spawns excessive algae growth, which can block sunlight and limit plant growth. Coastal areas that would otherwise be swaying in seagrass and kelp turn brown, murky, and barren of important marine species. But, not when sea otters are around.

Brent Hughes from the University of California, Santa Cruz and his colleagues studied 50 years’ worth of data, comparing areas with or without otters. The team discovered that otters trigger the above ecological chain reaction that protects seagrass meadows and can stave off algal blooms.

“The seagrass is really green and thriving where there are lots of sea otters, even compared to seagrass in more pristine systems without excess nutrients,” Hughes says.

Sea otters were hunted to near extinction in the 19^th and 20^th centuries. Populations on the California coast are slowly recovering now, and one of those places otters have called home since the 1980s is Elkhorn Slough, an estuary in Monterey Bay. Hughes and his colleagues determined that the re-colonization of that estuary by sea otters has been an important factor in the seagrass comeback.

In Tomales Bay, a nearby inlet with far lower levels of incoming nutrients, but no otters, the beds don’t look nearly as good. Hughes told Ed Yong of National Geographic:

The seagrass looks relatively unhealthy: it’s brown, covered in algae, and slumped over. The crabs are four times more abundant and 30 percent bigger than they are in Elkhorn Slough.

The findings in Elkhorn Slough suggest that expansion of the sea otter population in California and re-colonization of other estuaries will likely be good for seagrass habitat—and coastal ecosystems—throughout the state.

“This provides us with another example of how the strong interactions exerted by sea otters on their invertebrate prey can have cascading effects, leading to unexpected but profound changes at the base of the food web,” Hughes says. “It’s also a great reminder that the apex predators that have largely disappeared from so many ecosystems may play vitally important functions.”

The study was published last month in the Proceedings of the National Academy of Sciences.

(Sea otters also play a heroic role in the next Academy planetarium show! Currently in production and set for a fall 2014 opening date, the latest production from our visualization studio will highlight complex relationships in ecosystems—and how humans fit into the picture.)

Jami Smith is a science geek-wannabe and volunteers for Science Today.

Image: Robert Scoles/NOAA

Welcome to Sea Otter Awareness Week! Started 11 years ago to increase the public’s awareness about sea otters, the event “is an annual recognition of the vital role that sea otters play in the nearshore ecosystem,” according to seaotterweek.org.

Tomorrow we will explore that vital role a little more; for today’s article, we checked in with Moe Flannery, from the Academy’s Ornithology and Mammalogy department, to better understand the health of local sea otters.

The US Geological Survey’s Western Ecological Research Center conducts annual population surveys of the southern sea otter (Enhydra lutris nereis), a federally listed threatened species found in California. Flannery says the southern sea otter’s range extends from Pigeon Point near Half Moon Bay down to Point Conception in Santa Barbara County.

This year’s USGS survey was released earlier this month and the news is cautiously optimistic: sea otter numbers are up, due largely to an increase in the number of pups.

In its 2013 report, the USGS estimates the population to be 2,941. For southern sea otters to be considered for removal from threatened species listing, the population estimate would have to exceed 3,090 for three consecutive years, according to the threshold established under the Southern Sea Otter Recovery Plan by the US Fish and Wildlife Service. The USGS has been conducting the population surveys since the 1980s.

“Population growth in central California has faltered recently, so the fact that we’re seeing a slightly positive trend is a basis for cautious optimism,” says Tim Tinker, a USGS biologist who supervises the annual survey. “Certainly, sea otters have made an impressive recovery in California since their rediscovery here in the 1930s.”

“We counted a record number of pups this year, which led to the uptick in the 3-year average,” says USGS biologist Brian Hatfield, coordinator of the annual survey. “A high pup count is always encouraging, although the number of adult otters counted along the mainland was almost identical to last year’s count, so we’ll have to wait and see if the positive trend continues.”

USGS scientists also annually update a database of sea otter strandings—the number of dead, sick or injured sea otters recovered along California’s coast each year. Flannery leads the Academy as one of the organizations that responds to these strandings as part of the national Marine Mammal Stranding Network.

This year’s stranding number was 368. Flannery says that a remarkable number of sea otters wash up with shark bites. “The shark populations have been increasing because elephant seal populations are increasing,” she says. “The sharks appear to take a bite of the sea otters, but don’t consume them. As bony, skinny and furry as sea otters are (with up to one million hairs per square inch!), they’re probably less desirable than fat, blubbery elephant seals.”

Sharks aren’t the only threat to sea otters. Mainland diseases, such as toxoplasmosis from cat fecal matter, also plague the animals.

Because of their threatened status, all sea otter necropsies (animal autopsies) are performed by the California Department of Fish and Wildlife. However, many of the specimens end up here, in the Academy’s collections. The result is that we have the largest collection of southern sea otter specimens in the world. The number was up to 1,300 specimens last year, but several hundred have yet to be cataloged and processed, according to Flannery.

Researchers come from all over the world to study the specimens—last year scientists from UC Davis came to study dental pathologies in 1200 sea otter skulls!  They found that 93% of our southern sea otter specimens had problems with their teeth.

Luckily, most of us don’t have to study 1200 sea otter skulls to learn more about these engaging animals. For events around Sea Otter Awareness Week, including this week’s Nightlife at the Academy, click here. Celebrate!

Image: Mike Baird/Wikipedia

Here’s a round-up of recent science headlines we didn’t want you to miss!

Ancient Rivers

Without a smart phone or GPS device, how did early humans find their way out of Africa? A study published last week in PLoS One determines that ancient rivers, now covered by the Sahara Desert, provided habitable routes to follow.

Simulating paleoclimates in the region, the researchers found evidence of three major river systems that likely existed in North Africa 130,000–100,000 years ago, but are now largely buried by dune systems in the desert. When flowing, these rivers likely provided fertile habitats for animals and vegetation, creating “green corridors” across the region.

“It’s exciting to think that 100,000 years ago there were three huge rivers forcing their way across 1000-km of the Sahara desert to the Mediterranean—and that our ancestors could have walked alongside them,” says lead author Tom Coulthard of the University of Hull, UK.

Cosmic Beginnings?

Did life on Earth hail from Mars, as one researcher proposed last month, or comet collisions? Apparently, in both cases, it all has to do with the chemistry. Carl Zimmer, one of our favorite science writers, has a recent New York Times article about the chemistry needed to produce DNA from RNA. And while it doesn’t look like early Earth had those compounds, Mars might have.

Then, earlier this week, a study published in Nature Geoscience finds that the collision of icy comets with planetary bodies could result in the formation of complex amino acids, the building blocks of proteins (and life).

The researchers suggest that this process provides another piece to the puzzle of how life was kick-started on Earth, after a period of time between 4.5 and 3.8 billion years ago when the planet was being bombarded by comets and meteorites.

The team made their discovery by recreating the impact of a comet by firing projectiles through a large high-speed gun. This gun, located at the University of Kent, uses compressed gas to propel projectiles at speeds of 7.15 kilometers per second into targets of ice mixtures, which have a similar composition to comets. The resulting impact created amino acids such as glycine and D- and L-alanine. Sounds like a fun method of discovery…

Speaking of fun collisions, if you want more of them, the Morrison Planetarium at the Academy is featuring Cosmic Collisions in its current show rotation. From the our website:

Creative and destructive, dynamic and dazzling, collisions are a key mechanism in the evolution of the Universe.

Missing Mars Methane

One chemical Mars seems to be missing? Methane. The gas was sought as a possible sign of microbial life currently living on the seemingly barren world. However, despite earlier reports that NASA’s Mars rover, Curiosity, discovered methane on the red planet, NASA reports today in Science that none has been found.

Curiosity’s earlier evidence of methane detection turned out to be within leftover air from Earth. And previous reports of localized methane concentrations up to 45 parts per billion on Mars were based on observations from Earth and from orbit around Mars.

“It would have been exciting to find methane, but we have high confidence in our measurements,” says the report’s lead author, Chris Webster. “We measured repeatedly from Martian spring to late summer, but with no detection of methane.”

But don’t give up on microbial Martians just yet… “This important result will help direct our efforts to examine the possibility of life on Mars,” says NASA’s Michael Meyer. “It reduces the probability of current methane-producing Martian microbes, but this addresses only one type of microbial metabolism. As we know, there are many types of terrestrial microbes that don’t generate methane.”

Looking for extraterrestrial life? Next month’s Brilliant!Science festival can deliver it to you. Visit this page for more information.

Image: the Tunable Laser Spectrometer on-board Curiosity: NASA/JPL-Caltech

Yesterday we introduced you to four new species of Anniella, or legless lizards, found here in California.

The creatures, previously thought to be categorized under one species known as Anniella pulchra, were described in yesterday’s publication as separate, new species with their own name, range and type locality. Each species was named after a California naturalist that had some association with UC Berkeley’s Museum of Vertebrate Zoology (MVZ), home of co-author Ted Papenfuss; and the University of California Museum of Paleontology (UCMP), where co-author James Parham (now at Cal State Fullerton) was a PhD student. The biographies behind these taxonomic namesakes offer a fascinating glimpse into the history and impact of the museums. We thought we’d reveal their stories here today.

Anniella alexanderae is named after Annie Alexander. According to the MVZ website,

She was a naturalist, an intrepid explorer, and an extraordinary patron at a time when women did not have the right to vote and few had any involvement with the world outside their homes.

In 1908, Alexander donated $1 million in an endowment for the creation of the MVZ. The gray-bellied Anniella alexanderae is found in the southwestern San Joaquin Valley, near the town of Taft.

Alexander hired MVZ’s first director, Joseph Grinnell. The recently named purple-bellied species, Anniella grinnelli, is named after him. Even in the 1930s, Grinnell was concerned about conservation. From MVZ’s website:

As a visionary, he could see that the rich and unique vertebrate fauna of California was under siege from increasing impacts of human population growth and unsustainable land use practices.

Anniella grinnelli was discovered in a vacant lot behind the Home Depot in Bakersfield a few years ago. That lot is now developed. In yesterday’s paper, the authors placed the type locality for this species in a reserve that has been set aside to protect the endangered Bakersfield cactus.

Charles Camp was an undergraduate under Joseph Grinnell at the MVZ and later became director of UCMP, which was also created by Annie Alexander. Anniella campi, a yellow-bellied lizard with a double stripe, is named after Camp. In 1915, at the ripe age of 20, the young Camp discovered a new salamander species in California—“a major discovery because its nearest relative was found in Italy!” exclaims Papenfuss.

Anniella campi has the smallest range of all of the new California legless lizard species, occurring in just a few canyons that drain out of the Sierra Nevada Mountains and into the Mojave Desert. Papenfuss describes it as a relict: “It dispersed long, long ago when there were moister conditions.”

The yellow-bellied Anniella stebbinsi is named after Robert Stebbins, a herpetologist at MVZ, who was Papenfuss’s advisor. Stebbins, now 98 years old, grew up in the Santa Monica Mountains in southern California. It’s fitting, then, that Anniella stebbinsi’s range is the southern-most of the five California species.

Its type locality is at Los Angeles International Airport—no kidding. “The west side of the main runway at LAX,” Papenfuss confirms. “There are big sand dunes between the runway and the ocean, and the sand dunes are protected due to an endangered butterfly that lives there and nowhere else.” That’s good fortune for Anniella stebbinsi, too. “Everything else around that area is urban sprawl.”

Fascinating reptiles deserve fascinating names and homes!

Anniella grinnelli image: Alex Krohn

“You don’t have to go to remote places to find biodiversity,” says UC Berkeley’s Ted Papenfuss. “California has so much biodiversity we’re not even aware of.”

Papenfuss is talking about several new, colorful species of legless lizards that he and California State Fullerton’s Jim Parham describe in a new paper, out today in Breviora, a Harvard publication.

Legless lizards, or Anniella, are “cuter than snakes,” says Parham and also distinctive from the other, better-known legless reptiles. For example, “Anniella have eyelids—snakes don’t,” Parham explains. “Legless lizards, like other lizards, can also lose their tails to escape other predators,” adds Papenfuss. “Snakes unhinge their lower jaws to eat their food whole. Lizards, including Anniella, have to chew their food.”

Parham and Papenfuss published a paper in 2009 about a known California species, Anniella pulchra. Through genetic testing of new specimens and museum collections, including the Academy’s, they determined that there are likely more than just the one species of legless lizard here in California. Today’s paper describes four new species.

Confirming the previous genetic work, the team identified Anniella alexanderae, Anniella campi, Anniella grinnelli and Anniella stebbinsi, each occupying a distinct geographical range. The previously known species—Anniella pulchra—has a yellow belly, and the new species have yellow, silver, or purple bellies. The new species can be further distinguished visually by their number of scales or vertebrae. But, the main difference is determined by DNA, which shows that these species diverged from each other millions of years ago.

As Papenfuss noted above, biodiversity can hide in the most obvious places (such as California), but that doesn’t mean it’s easy to find. The trick with these animals is they live underground. They can often be found under logs or leaf litter where there will be some dampness and insects to eat. But, logs and leaf litter aren’t always present in the sand dunes, deserts and grasslands Anniella prefer.

So Papenfuss invented his own “litter”—literally, says Parham. “He’s essentially littering, with permission.” Papenfuss admits he “dumpster dives” on the UC Berkeley campus looking for cardboard. He uses the flattened pieces as man-made leaf litter in the places he thinks Anniella like to hide and leaves the litter out for months as at time. However, he learned quickly to cover the cardboard with some tarpaper, because cows were eating the uncovered cardboard.

Despite today’s publication, Papenfuss isn’t finished dumpster diving. “This is only the beginning of the story,” Parham says. “We need to further study each species’ distribution. At this point, each species has quite small ranges and if that’s truly the case, more monitoring of their habitat needs to be done. If we lose those small spaces, we’ll lose those species.”

Citing human development such as urbanization, agriculture, and oil/gas exploration as threats to the species, the team realizes they’ll have to work quickly to determine where these species occur and how to protect them and their habitats.

By the way, do the new species’ names sound familiar? Each is named after a famous California naturalist—tomorrow we’ll look at the namesakes and ranges for each new species.

Image: James Parham

The period on our planet between 540 and 520 million years ago when most modern animal groups appeared is also known as evolution’s Big Bang. Prior to the Cambrian explosion, life was much simpler on Earth—single-celled organisms dominated the landscape.

But how did so many different organisms develop in such a short period of time? “The abrupt appearance of dozens of animal groups during this time is arguably the most important evolutionary event after the origin of life,” says Michael Lee of the University of Adelaide. “Darwin himself famously considered that this was at odds with the normal evolutionary processes.”

Lee and his colleagues decided to look into “Darwin’s dilemma,” focusing on arthropods (insects, crustaceans, arachnids and their relatives), the most diverse animal group in both the Cambrian period and present day.

“It was during this Cambrian period that many of the most familiar traits associated with this group of animals evolved, like a hard exoskeleton, jointed legs, and compound (multi-faceted) eyes that are shared by all arthropods,” explains team member Greg Edgecombe of the Natural History Museum of London. “We even find the first appearance in the fossil record of the antenna that insects, millipedes and lobsters all have, and the earliest biting jaws.”

The team quantified the anatomical and genetic differences between living animals, and established a timeframe over which those differences accumulated with the help of the fossil record and intricate mathematical models.

“In this study we’ve estimated that rates of both morphological and genetic evolution during the Cambrian explosion were five times faster than today—quite rapid, but perfectly consistent with Darwin’s theory of evolution,” Lee says.

ScienceNOW offers the numbers:

The creatures’ genetic codes were changing by about .117% every million years—approximately 5.5 times faster than modern estimates.

Unusual, perhaps, but in line with natural selection, the team indicates. The study appears in the recent edition of Current Biology.

Perhaps Darwin can get some rest now.

Image: Michael Lee

Here’s a sampling of a few science headlines from this past week—enjoy!

Grey wolves

When are grey wolves not grey wolves? According to headlines this week in Nature News and New Scientist, the grey wolves are called eastern wolves when the US Fish and Wildlife Service (FWS) wants to de-list the animals from the Endangered Species list.

Citing a publication in FWS’s own North American Fauna journal, the agency claims that the grey wolves were never historically in the regions where the species are being restored. Those were a separate, healthy species, eastern wolves.

But scientists, not to mention genetic testing, describe the eastern wolves as a sub-species of grey wolves. Read more about the science and politics in Nature News.

Crazy, dangerous fungi reproduction

Cryptococcus neoformans is a dangerous fungus that infects individuals with compromised immune systems, such as HIV/AIDS patients. It causes more than 600,000 deaths a year, accounting for a third of all AIDS-related deaths. Some strains can be drug resistant and scientists had a hard time determining why.

Like some other fungi and microorganisms, C. neoformans are both asexual and procreate with exact replicas of themselves, where the expected outcome should simply be more of the same. So how could some individuals develop drug resistance when others do not?

Now researchers, publishing in PLoS Biology, have found the act of sex between such genetically identical organisms can itself be mutagenic, meaning it can create genetic changes and diversity where it did not previously exist. In fact, in the case of the fungus C. neoformans, the process of sexual reproduction can result in extra bundles of genetic material or chromosomes that can be beneficial to the organism’s survival—such as drug resistance.

ScienceNOW has more information.

The chemistry behind whiskey

Thank goodness for Thomas Collins (that’s really his name!) of UC Davis. He’s studying the chemical compounds that make up rye and bourbon whiskeys.

Using chemistry’s latest analytical tools, Collins’s team profiled 60 American whiskeys and found that a single whiskey sample can contain hundreds of nonvolatile compounds, the ones that tend to stay in the liquid rather than evaporate off. Added up across multiple samples, the number of compounds comes to about 4,000 total, a scientific testament to the complex molecular mingling that occurs as a spirit ages, sometimes for decades, in a 53-gallon oak barrel.

Why the in-depth study? “Whiskeys’ chemical profiles could be used for distillers’ quality assurance or process improvement programs,” says Collins, who has conducted similar experiments on wine. “In addition to that, they could be used to help speed up production.”

I’ll drink to that! NPR has more details on the influence of oak barrels on whiskey flavor.

Image (fungus): Joseph Heitman