Turtles are more closely related to Crocodiles than Lizards!

CREDIT: G. GRULLÓN/SCIENCE
The orange line shows where turtles actually belong in this part of the tree of life, the dashed lines indicate previous suggestions.
New DNA techniques have recently been developed to more easily determine where species belong in the tree of life. See Large-Scale Gene Comparisons Boost Tree of Life Studies in Science. As you may have heard, birds and dinosaurs are closely related. Moving further up the tree, Archosaurs are a group that contain birds, dinosaurs and crocodiles as well as the extinct flying reptiles, the Pterosaurs. Thanks to this new research, turtles are now known to be the sister group to the archosaurs.
A red-eared slider.

Manta Trust

Giant Mantas are my favorite creatures of the sea, here's a photo one of my favorite encounters from 2010:
photo by Sten Johansson
I just learned about the web site Manta Trust from Daniel Fernando, who I met in Sri Lanka last year. Daniel is a marine biologist and is very knowledgeable and dedicated to manta conservation. He is based in Sri Lanka - a beautiful country which has abundant and varied marine life but limited resources at this point in its development and history.


The Manta Trust web site is an excellent source of information about manta rays and conservation.
Here's one of my previous blog posts on mantas.

Allergies

There's a special section on Allergies in Nature magazine this week. That holds special interest for me personally since I'm allergy prone. I've been violently allergic to eggs since I was an infant - for example, I can't have vaccinations cultured with eggs including flu vaccines. When I was 19, before I knew that some vaccinations were cultured in eggs, I received one and then spent a week in the MIT infirmary - I needed two shots every 15 minutes for the first 36 hours just to keep me alive - ouch!
I had asthma as a child, but grew out of it. I developed an allergy to cats and many other furry animals (but not dogs) while in college - I would walk into a room with a cat and in seconds start sneezing and rubbing my eyes. But that's been much less severe since my early forties. I developed hay fever in my mid-thirties which persists but it seems to be getting somewhat less severe. I also seem to have developed allergies to kiwis and avocados, both of which I loved growing up, both of which I unknowingly ate mixed with eggs (kiwi sherbert and guacamole) during my thirties and ever since have experienced strong reactions.

Atophy: Marching with allergies in Nature is written by an individual tormented by a wide array of allergies. The author also suffered from chronic eczema, one annoyance I've been mercifully spared.


Food: Picky eaters discusses food allergies, including the possibility of creating tolerance by ingesting tiny amounts of the allergen and gradually increasing the dosage.

How do porcupines make love?

This riddle appears in the 1987 film Black Widow starring Debra Winger and Theresa Russell.
The two main characters are: women; formidable adversaries; and they are stronger and more clever then the men in the story. They use men to further their goals - kindly in one instance, cruelly in another - but they control their own destinies.
Any other good examples of stories - filmed or written - along those lines?




The article How do porcupines make love? from Annals of Improbable Research, reveals the punch line to the joke and then goes on to detail the actual mating behavior of these mammals - your previous ignorance of you may come to cherish.




When I was a little kid, nine or so, I had heard the f-word, realized of course, it was probably something naughty, but didn't yet know the actual definition. I finally asked another kid, who disdainfully outlined the concept. "Oh," I responded, "you mean copulation?"

Leonardo's Rule

Leonardo da Vinci observed that

all the branches of a tree at every stage of its height when
put together are equal in thickness to the trunk

There have been various attempts to explain that, involving the tree's vascular system for example. The preprint Leonardo's rule, self-similarity and wind-induced stresses in trees votes for wind resistance. See also Leonardo's Formula Explains Why Trees Don't Splinter at Science Now.

Guarding the Germline

The great apes (humans, gorillas and chimps) are able to reproduce for many decades -longer than other primates. Researchers have discovered a genetic change which is active in human testis that helps guard the genome and ensure the quality of sperm. See the original report Endogenous retrovirus drives hitherto unknown proapoptotic p63 isoforms in the male germ line of humans and great apes in PNAS and Those retroviruses get everywhere at the MicrobiologyBytes blog.
It wasn't clear to me if this also occurs in Orangutans, the paper said the change occurred about 15 million years ago and the Orangutans diverged 12-16Mya Comparative and demographic analysis of orang-utan genomes. Female orangutans are fertile for 30 years, fairly similar to human females. What about the males?

Video of Mantis Shrimp doing Somersaults!

From the underwater filming experts Scubazoo.
See also Mantis Shrimps are Really, Really Cute and New Form of Vision Discovered for more about mantis shrimps.

Extinctions and Ocean Anoxia

There were a series of massive extinctions during the Cambrian period around 500 million years ago, the period when the first modern animals are found. There is new evidence that the extinctions coincided with dramatic decreases in ocean oxygen levels: Biogeochemistry: Toxic Cambrian oceans in Nature.

Origins of Life at Higher Temperatures

Modern biology depends on an intricate web of chemical reactions, many of which are vastly accelerated by enzymes, which themselves are typically large molecules made by complicated machinery. How did this extraordinary network manage to evolve from a nonliving environment? This paper in PNAS, The Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes, points out in that many important biochemical reactions proceed much faster in higher temperature environments, which might have been typical in the early earth.

How Cats Drink

I had always heard that the raspy hairs on the cat's tongue were what enabled it to lap up water so neatly. Not at all. The cat flicks the tip of its tongue into the water which shoots up a stream of water and the cat, with perfect timing, closes its jaws over the stream to capture it - four times a second! See For Cats, a Big Gulp With a Touch of the Tongue in The New York Times

Oxygen increase in the Devonian Period

There's new evidence of a substantial increase in ocean oxygen content during the Devonian period about 400 million years ago.  That was around the time that vascular plants arose, so perhaps that's what caused the increase.  At the same time more complicated animals such as predatory fish evolved  - so perhaps the higher level of oxygen is what made that possible.   See Plants set stage for evolutionary drama in Nature.

Codons matter

DNA codes for amino acids with triplets of bases (codons). There are four different bases and hence 64 different triplets. There are typically twenty different amino acids (plus start and stop signals) which need to be coded, so there is some redundancy - a single amino acid can have multiple codons which are all translated the same way. However, there is now evidence that the actual codon may make a difference. New Roles for Codon Usage in Science reports that two very similar but distinct proteins are modified differently, depending on the original codon.

Picophytoplankton

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton in PNAS.

Small (2-3μm) uncultured photosynthetic eukaryotic plankton (picophytoplankton) are a substantial component of the biomass and primary production in the oceans. Pico-prymnesiophytes genomes seem to be a mosaic, with the chloroplast and nuclear genomes from different lineages.

The Mystery of Sea-Floor Methane

The Ongoing Mystery of Sea-Floor Methane in Science.

Each year, ocean sediments produce a quantity of methane equivalent to about half of the methane emitted to the atmosphere from all natural sources (1). Very little of the methane produced below the sea floor, however, reaches the ocean or the atmosphere; most is consumed by anaerobic microorganisms as it diffuses up through oxygen-poor (anoxic) sediments. Researchers recognized this process, known as anaerobic methane oxidation (AMO), nearly 35 years ago (2), but it remains poorly understood. Investigators have not been able to firmly establish the reaction mechanism, fully understand the factors that control oxidation rates, or isolate the responsible organisms. This represents a gaping hole in our understanding of one of Earth's primary sinks for methane. Recent studies of a rare but intriguing sedimentary environment–sea-floor seeps of methane-rich fluids–have provided new insights into the microorganisms that inhabit methane-rich sediments, but raised new questions regarding reaction mechanisms.

Field Testing Sexual Selection in Crickets

Dance Like No One Is Watching, Sing Like No One Is Listening? in Science.

Genetic paternity testing and field observations of crickets challenge conventional wisdom about sex differences and fitness.

Ultrasmall Archaea

Enigmatic, ultrasmall, uncultivated Archaea in PNAS.

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge—particularly for Archaea—that occur at relatively low abundance and in extreme environments. Ultrasmall cells (< 500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal>/euryarchaeal divide have been detected in a variety of acidic ecosystems.

Manta Rays

Once again I've had the good fortune to visit the Manta Rays of San Benedicto Island, in the Pacific off the coast of Mexico. Thanks again to Gregory Colbert, his film crew and friends, and the crew of the Nautilus Explorer for another wonderful trip.
I haven't been able to find a reference to the tubes just above the corners of the manta's mouth pictured below. Thanks to Sten Johansson of the Nautilus Explorer for the photos and for pointing out this interesting feature. Please comment if you can identify these structures, a reference or link to the literature would be especially welcome!

Prospects for Personal Genomics

Multiple personal genomes await by J. Craig Venter in Nature. Gene sequencing pioneer Venter reviews the current state of the art. One difficult problem is due to chromosomes occuring in pairs, one from each parent. Apparently it isn't easy to distinguish the two copies and the differences between them.

Chemistry of the Ancient Oceans

Ocean Chemistry and Early Animals in Science. Animal life requires oxygen. What stages took place before the current oxygenated ocean chemistry and animal communities beccame established around 542 million years ago?

Arthropod Phylogeny

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences in Nature.

The evolutionary interrelationships of arthropods has long been a matter of dispute. A new phylogeny applies an arsenal of techniques to more than 41,000 base pairs of DNA from 75 arthropod species. The results support the idea that insects are land–living crustaceans, that crustaceans comprise a diverse assemblage of at last three distinct arthropod types, and that myriapods (millipedes and centipedes) comprise the closest relatives of this great 'pancrustacean' group

See also Surprising New Branches on Arthropod Family Tree
The the newly defined sister group to the Hexapoda (insects and related species) is the Xenocarida or strange shrimp some unusual recently discovered marine crustaceans. So insects are actually more closely related to some oddball marine crustaceans than other terrestrial arthropods such as spiders.