Moving on up...

Hi all.

Exciting news.  I've started a new palaeo blog with a co-author; my good friend David Button who is studying for a PhD at the university of Bristol.  You can find the new and improved site here.

I'm excited about this new blog.  The science is better, the format is better and with Dave's additional perspective I think it will be a more interesting read.  I hope to see you all there.

Cheers.

Joe.  

Sea squirt - Dave Wells. 3

Do It Yourself Cladogram

So as promised, we will be constructing our own evolutionary trees. Please download the file.

As you can see we have included 6 taxa in our phylogenetic analysis. We can identify a number of variable characters which can be used to distinguish between each taxon. Table 1 lists these characters and also states whether each character is primitive or derived. When dealing with fossil taxa it is often difficult to discern whether the character you are examining is a primitive or derived state (in other words whether a character appeared early or late in the evolutionary history of the group of organisms you are examining). For example, within reptiles, snakes lack limbs. This is a derived character within reptiles because reptiles primitively possessed limbs (reptiles evolved from amphibian-like ancestors which possessed 4 limbs).

Within this example, we will assume that the polarity of the characters (that is whether a character is primitive or derived) has been determined in a previous study.

So let’s get building our tree!

STEP 1

Table 2 lists each taxon and each character. Access whether each character exhibits a primitive or derived state within each taxon. Mark a primitive state with 0 and a derived state with 1. If the character is not applicable for a certain taxon, mark with a ?. In the last column, add up every 1 for each taxon. This will give you the derivation state for that taxon.

STEP 2

In table 3, rank the taxa in order of their derivation state (1st=highest etc.).

STEP 3

For each of the derived character states in the first column of table 1, list all taxa which possess that character.

STEP 4

Using both tables 3 & 4, draw a cladogram to show the interrelations of the taxa.
Tips:

- The derivation state should increase as you move up the cladogram.

- A cladogram should divide from 1 branch to 2 branches.

- Try to group the most exclusive groups first (that is the groups from table 4 that have the fewest members).

There are two cladograms that fit the available data fairly well. Once you have completed the cladogram, compare yours with the examples below.

Answers

Sea squirt - Dave Wells. 2

Phylogenetics for Beginners

What is phylogenetics? Wikipedia says "the study of evolutionary relatedness among various groups of organisms which is discovered through molecular sequencing data and morphological data matrices". A less ridiculous way of saying this would be "the study of relations between organisms through comparison of genetic or morphological (form and structural) information. Phylogenetics assumes evolution is a branching process whereby a population of organisms which have become separated for some reason, be it geographical or behavioural, undergo evolutionary change through mutation and natural selection.

We can build phylogenetic trees to help understand the order of branching, representing the pattern of evolutionary diversification, within a particular group of organisms. Phylogenetic trees are constructed using a method called cladistics, which assigns organisms with shared derived characters (synapomorphies) to groups called clades. As palaeontologists cannot access genetic information for extinct organisms, we use morphological characters as synapomorphies.



Fig 1. Click to expand.

This is a phylogenetic tree of extant vertebrates which serves as a good example of which sort of groups are useful and informative and which aren't. Clades are, by definition, monophyletic. This means that the group contains all descendants of a common ancestor. Birds are a clade united by the presence of synapomorphies such as feathers. Node no. 1 on the diagram is also a clade. This is Osteichthyes - the bony fish, which are united by synapomorphies such as a bony skeleton. Although the name suggests that the group contains just fish, Osteichthyes is a monophylectic group therefore must contain all the descendents, including amphibians, mammals, lizards, crocodiles and birds. In fact, each node on the tree defines the base of a monophylectic group (if you’re interested the clades are, in ascending order, osteichthyans, tetrapods, amniotes, diapsids, archosaurs).

Traditionally, the class ‘reptiles’ excludes birds. On our tree we could group lizards and crocodiles together as 'reptiles'. This however is a paraphyletic group as it excludes one or more descendent. Paraphylys are thought to be of limited use, primarily because they are more difficult to define than monophylys. However, they are sometimes useful when discussing evolutionary transitions, as we shall explore at a later date. The worst of the worst are polyphyletic groups. The most obvious one on the tree above is 'warm blooded'; a grouping of mammals and birds which has no evolutionary significance whatsoever. In fact the ability to maintain thermal homeostasis evolved independently within each group. Polyphyletic groups are nonsense groups with no relevance to evolutionary relationships.

Through phylogenetics we can begin to build a picture of how vertebrates evolved. For example, we know that tetrapods (node 2) are defined by synapomorphies such as limbs with digits and sepertation of the head and forelimb. Therefore we can infer that these major evolutionary changes must have occurred between nodes 1 and 2 on our tree. This might seem a lot to take in, with lots of difficult terminology, but a working knowledge of phylogenetics will be essential for future posts. In the immediate future however, I hope I can consolidate phylogenetics by teaching you how to build your own phylogenetic trees. I always learn best when doing.

Sea squirt - Dave Wells. 1

Rising from the smouldering ashes like a phoenix, ALL THE TIME IN THE WORLD is back!

This is the first in a series of posts exploring our origins as vertebrates from backboneless swimming squirts to the masterful primates we are today. The motivation for this is twofold:

1)To give my reader/s an insight into the science behind vertebrate origins, as well as evolution in general, from the perspective of a palaeontology student.

2) To give me another reason to do some serious background reading as I go forth into terrifying PhD interview territory.

These posts will hopefully address some important questions about vertebrate evolution and diversification. For example;

What is a vertebrate and what isn’t? Where do you draw the line?
What do we know about the origin of vertebrates? How, where and when did they evolve?
What are the closest living relatives of vertebrates?
When did bone/teeth evolve?
When did jaws evolve? (Bizarrely a separate issue from teeth)
What is ‘Dunkles bony one’?
When did sharks evolve?
What is the difference between a goldfish and a coelacanth and why is this important?
When did our ancestors first crawl out of the water? How and why did limbs evolve?

Ultimately, this blog series will attempt to explain how palaeontologists go about reconstructing the tree of life from often scant and meagre fossil material. It would be nice if these posts have some general appeal to anyone stumbling upon this blog, so I’ll do my best to make it both informative, entertaining and, most importantly, regular.


Fig. 1. The tree of animal life. Although simplified it helps to illustrate the astonishing diversity of multicellular life. Our whirlwind evolutionary adventure will take us from basal deuterostomes to mammals, with lots in between.

Castle of Terrible Doom!

I realise that I haven’t posted in a while, so I've prepared a special treat for all my eager readers. I've made a game! It’s totally free, and you can download it here.

It's in the style of a 'choose your way' adventure, simply load it up on Powerpoint and click the play from beginning button under the slideshow tab.

I realise there is a danger that this game may shock and offend anyone who should chance upon this blog, so if you are of the politically correct mindset, I advise you not to play.

For those that choose to brave the game, good luck.

P.S. Hint - there is a clue in the kitchen.

Denizens of the Deep

A week or two ago, my good friend, Mr David Wells B.A. (Hons), and I got onto the topic of deep sea gigantism. To the casual reader, this may seem an absurd topic of conversation and for the life of me I can’t remember how we got on to it. However, such conversations are all to frequent between our group of friends; admittedly I am mostly to blame. Never the less, I feel that deep sea gigantism merits a revisit, especially as it gives me a chance to post some photos of the most charmingly hideous creatures known to man. Pardon the pun, but I’ll dive right in.

This many legged friend is a Giant Isopod. It’s a type of crustacean closely related to woodlice. Here it photographed next to a bewildered cat for the entertainment of some Chinese people.

Here is another frightening arthropod. The Japanese Spider crab, photographed here with a smiling man scale bar, can attain a leg span of 3.8m.













Many deep sea squid species attain a colossal size. The biggest of them all is the appropriately named Colossal Squid (Mesonychoteuthis), which can be found in the Southern Ocean. The photo above was originally believed to be first image of the elusive giant squid (Architeuthis). It has since been re-identified as a Robust Clubhook Squid, another large squid species.

It's not just invertebrates that grow to extreme size in the deep. Vertebrates too can attain monstrous proportions. The Pacific Sleeper Shark and the bizarre Megamouth Shark rival the Great White in length. However, the champion of champions, and my personal favourite, is the King of Herring (pictured above). It’s a species of Oarfish, which are essentially elongate bony fish (unlike sharks which have cartilaginous skeletons). The King of Herring is listed by Guinness as the longest bony fish in the world and can reach a whopping 17m.

Deep-sea gigantism is when some animals become much larger than their shallow-water or terrestrial relatives. The question is why gigantism is commonplace in the ocean depths. There is a general consensus that limited food availability plays a crucial role in encouraging gigantism in the deep sea. Competition for limited resources results in natural selection of an optimal body size for a particular habitat. In many ways, this idea is similar to that of Island gigantism (e.g. Galapagos Giant Tortoises). However, the key difference is that Island gigantism relies on the removal of typical apex predators and dominant herbivores (e.g. large mammals) leaving other organisms free to increase in size. Such a situation seems less likely within oceans. After considering this, it seems paradoxical that a constrained food source would result in larger body size within the deep sea realm. However, I think the fact that the cause of deep sea gigantism remains a mystery only enhances the enigma of these denizens of the deep... And yes, that was a magic the gathering reference.