Archive for Bonnan

Along the Backbone is not forgotten … just dormant and undergoing updating

Posted in Along the Backbone Information with tags , , , , on June 13, 2013 by Dr. Matt Bonnan

Since my last post on Along the Backbone, things have changed.  How so?  Well, read here to find out:

This site is not defunct, but it is undergoing a major overhaul to update it to my new position.  The audio files have to be reconfigured as well in order to update them with my current information.

At some underdetermined but not far-off future point, the podcasts will be re-released and new material will begin to surface.

In the meantime, I hope all visitors to this site will use and enjoy what I have already made available.

Thanks for your patience.


Is there a topic you’d like to see covered on Along the Backbone?

Posted in Along the Backbone Information, Along the Backbone Polls with tags , , , , on February 22, 2012 by Dr. Matt Bonnan

Is there a topic you would like to see covered on Along the Backbone?  Post your comments in this topic thread and let me know.  In the meantime, I will continue to produce new episodes on a variety of evolutionary anatomy topics, from brains to bones, across deep time.

Help select the next story you hear on “Along the Backbone”

Posted in Along the Backbone Polls with tags , , , , , , , on November 1, 2011 by Dr. Matt Bonnan

Time for some feedback: influence which story is produced for “Along the Backbone”:

The polls will close Friday, November 4, at 12:00 midnight!

Episode 5: Elephants, Cats, and Ticking Clocks

Posted in Individual Podcasts and Transcripts with tags , , , , , , , , , , , on October 24, 2011 by Dr. Matt Bonnan

Unlike a lizard where the limbs are sprawled out to the sides, most mammals have drawn their limb bones vertically beneath the body.  What are the functional advantages of such a posture? And what does all this have to do with Dr. Bonnan almost being creamed by an African elephant?

Podcast Teaser: I learned the real meaning of the word “awesome” during a close encounter with an African elephant.  A colleague and I were in an animal park in South Africa, and we had spied a large, lone male elephant walking towards our car.  As I was taking pictures of the elephant, our car was suddenly traveling in reverse with my colleague uttering frantic expletives.  It was at this point I noticed that the elephant was picking up speed and coming right for us.  On attempting to turn the car around, we became stuck, and now our fate was left to a very large mammal.  In my cleverness, I rolled up the car window, as if that would protect me from 6 tons of muscle and bone!

References / Further Information

Episode 4: A Brief History of Meat

Posted in Individual Podcasts and Transcripts with tags , , , , , , , , , on October 14, 2011 by Dr. Matt Bonnan

Many of us enjoy eating meat, but few of us pause to think about how important its pre-meal form, skeletal muscle, is for vertebrate life.  Or why you eat different parts of fish and tetrapods for that matter.

Podcast Teaser: I don’t know about you, but I enjoy a good steak, especially fillet minion.  In fact, many of us enjoy eating meat, but few of us pause to think about how important its pre-meal form, skeletal muscle, is for vertebrate life.  Unless you injure your skeletal muscles, you barely notice them – of course, if you’re a body builder, you probably notice them a lot more.  But the contractions of skeletal muscles across the joints in your skeleton do everything from keeping you upright to preventing nasty falls.  Believe it or not, meat is so universal among vertebrate animals that muscles in one area in a fish do very similar things in the same area in your body.  This is because, long ago and 540 million years away, our common ancestor developed two important traits …

References / Further Information

Transcript Available Upon Request.

Episode 3: How Do You Make a Snake?

Posted in Individual Podcasts and Transcripts with tags , , , , , , , , , , on October 11, 2011 by Dr. Matt Bonnan

It seems only fitting that a podcast series called Along the Backbone should discuss the formation of the backbone in one of lengthiest vertebrates: snakes.

Podcast Teaser: Snakes are lizards.  More specifically, snakes are limbless, eyelidless, earless lizards with megakinetic skulls and well-developed salivary glands that often produce venom.  Among the many standout features of snakes, perhaps the most fascinating is how these vertebrates routinely develop a body that will have 120 or more rib-bearing vertebrae and no limbs.  It turns out that a simple but profound difference in the timing of the expression of developmental genes called HOX genes renders snakes limbless, whereas an increase in the frequency of another set of clock-like genes generates their amazing number of vertebrae.

References / Resources:

Transcript available upon request.

Episode 2: Why Pedigrees Are Not Just For Dog Shows

Posted in Individual Podcasts and Transcripts with tags , , , , , , , , , , , , , , , on October 10, 2011 by Dr. Matt Bonnan

When we talk about reconstructing the vertebrate family tree, we are also trying to develop a pedigree of relationships. This pedigree, in turn, helps us understand how anatomical changes have taken place over time.

Transcript of Episode 2: Why Pedigrees Are Not Just For Dog Shows

Our family has a miniature pinscher named Squirrelbella.  You can ask my six-year old daughter about that name.  Squirrel, for short, is no show dog, and so as much as we love this little tail wagging, occasionally yippy carnivore, we do not have pedigree papers for her.  In the world of dog shows, pedigrees are important to establish the blood line of the dogs which end up being winners.  To make future money, you as a serious breeder would want to have offspring that descended from the winners and not the losers.  In short, you want a reliable pedigree: a family tree.

When we talk about reconstructing the vertebrate family tree, we are also trying to develop a pedigree of relationships.  Formally, such a pedigree of relationships is known as a phylogeny.  A phylogeny is a hypothesis of relationships, based on data, which is open to testing and which predicts the shared common ancestry of various groups.  This means that any phylogeny is not permanent – it will either be supported, modified, or rejected when new data surface.

If our goal is to understand how vertebrate form and function has changed in different groups, or even to define what a vertebrate is, we have to understand the order and appearance of these skeletal features.  For vertebrates, we typically reach an understanding of changing function by comparing the anatomy of several related groups to see what has changed (what traits are special to our group of interest) and what has remained the same (what traits are present in all vertebrates).  This requires an understanding of the relationships of vertebrates.

We establish vertebrate phylogeny on traits, the attributes or features of particular animals.  Simply put, a phylogeny is a hypothesis of relationships established using trait data.  But traits are not self-evident – they are not labeled neatly on fossils or written on the tags of pickled museum specimens.  So, how do we select informative traits?

The simplest approach to reconstructing vertebrate phylogeny would be to survey as many animals as possible and then compare the distribution of similar traits.  We could then tabulate up all the similarities, and group together vertebrates which share more traits in common.  For example, we group all known vertebrates together because they all possess specialized back bones called vertebrae.  We could continue comparing similar traits, divvying up the vertebrates into smaller subgroups possessing more exclusive shared traits.  Fish have gills, amphibians have a moist skin, reptiles are scaly, birds have feathers, and mammals have hair.  By doing this, we would eventually have a phylogeny, a hypothesis of relationships among the living vertebrates.

Yet, not all similar-looking traits are related to common ancestry.  For example, a shark and a dolphin both have a stream-lined body form with fins.  At face value, we might conclude that these traits were evidence that sharks and dolphins shared a recent common ancestor.  However, on closer inspection, we would begin to notice some large discrepancies.  The skeletal structure of the shark is cartilaginous whereas that of the dolphin is bone.  A shark’s skin is rough and covered in tooth-like scales, yet that of a dolphin is smooth and overlies a layer of blubber.  Sharks breathe using gills, but dolphins have lungs and must surface occasionally to take in fresh air.  Dolphins nurse their young on milk from mammary glands while shark pups must fend for themselves.

Eventually, it would occur to us that, more likely, the similar shapes of the shark and dolphin were not due to common ancestry but instead to a common environment: water.  Water is denser than air, and there are only so many “solutions” to swimming fast in it.  The shark and dolphin have converged onto a similar functional solution, the streamlining of their bodies and the possession of fins, to move fast in a dense medium.  So, overall similarity is not good enough: we must be able to distinguish between traits inherited through common descent and those that are due to convergent evolution.

Traits are not static.  Under the theory of biological evolution, traits are inherited and modified during descent from a common ancestor.  Traits, the key features we are establishing vertebrate relationships on, are plastic and malleable – to wit, they change.  Although the plasticity of traits seems at first to be a stumbling block to establishing vertebrate phylogeny, it is in fact a great asset.  This is because traits have states – that is, they have an original form and one or more variant forms inherited and passed down to different descendants.

The original form or state of a trait is referred to as primitive, whereas a trait is considered to be in a derived state if it has changed from this original condition.   It is the change from the primitive to the derived trait state which reveals evolution and pedigree.  For example, one type of trait is that of possessing appendages.  The appendages of the earliest jawed vertebrates were fins.  Therefore, fins are the primitive appendage state, and modern jawed fishes would be said to retain the primitive appendage condition.  In contrast, amphibians, reptiles, birds, and mammals have changed the original condition (a fin) into a new structure (a limb with digits).  So, in this example, fins are the primitive (original) appendage type, and limbs with digits are the derived (changed from the original) appendage type.  All vertebrates possessing the derived appendage state of limbs with digits are grouped together as tetrapods.  We would hypothesize that all tetrapods share a closer common ancestry with each other than any of these animals would with fishes.

The word primitive is often confused with something inferior or less developed.  It is important to note that all living vertebrates today actually possess a complex combination of primitive and derived traits.  To dispel you of equating a primitive trait with inferiority, imagine being thrown into a tank with a hungry shark.  Yes, the shark has primitive appendages (fins), and you have derived appendages (limbs with digits), but which of you will swim well?  Which of you will be the diner, and which the dinner?

But how does one determine whether or not a trait is in its primitive or derived state?  The answer is something called polarity.  Because trait states are changeable, they have polarity, or a direction of change from primitive to derived.  Polarity is an arrow of change pointing in the direction that a particular trait evolved.

Polarity is inferred in a number of ways.  In one approach called outgroup comparison, the trait state of interest is noted over a large number of animals outside the ones being studied.  If one particular state is widely distributed over these so-called outgroups, the researcher may conclude that this is the primitive state.  This reasoning would follow from evolutionary theory: all vertebrates should share certain general trait states, followed by different descendant groups that possess more exclusive trait states.  Therefore, commonality may indicate that a particular trait is in its primitive state.

Another approach to determining trait polarity would be to note when certain anatomical features appeared during embryonic development.  The idea here is that more general, foundational trait states should appear earlier in development, whereas more derived states of various traits should develop at a later time.  For example, all vertebrate embryos develop throat (pharyngeal) slits during development, but these are only retained as spaces for gills in fishes; the slits anneal and contribute to other structures in tetrapods.  Since all vertebrates develop these pharyngeal slits before these features transform into more specialized structures within each group, the retention of these slits in fishes would be considered primitive, and the annealed versions would be called derived.

The modern biologist or paleontologist thus collects trait state data and, using specialized software, analyzes the distribution of primitive and derived trait states.  The relationships of the vertebrates are determined by how many derived trait states they share in common, and this is translated into a branching diagram of relationships: the phylogeny.

The phylogeny is established on trait states that are independent of the chronological order of their appearance in the vertebrate fossil record.  This means that the fossil record can serve as an independent check or test against the phylogeny.  Since the assigned polarities are hypothetical, the chronological sequence of when certain trait states appear in the fossil record can either support or call into question whether something is indeed primitive or derived.  For example, the earliest jawed vertebrates in the fossil record possess fins, whereas it is not until much later that we see the first fossil vertebrates possessing limbs with digits.  This observation independently bolsters the assignment of fins to the primitive appendage state.  Through careful analysis of both traits and the fossil record, a reasonably consistent phylogeny of vertebrate animals has emerged, even if my little min pin doesn’t appreciate it.