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3.3: Fossils and family relationships: introducing cladistics - Biology


As mentioned previously, we continue to discover new fossils and new organisms. We can expect there are dramatic differences between the ability of different types of organisms to become fossilized.61 Perhaps the easiest organisms to fossilize are those with internal or external skeletons, yet it is estimated that between 85 to 97% of such organisms are not represented in the fossil record. A number of studies indicate that many other types of organisms have left no fossils whatsoever62 and that the number of organisms (at the genus level) that have been preserved as fossils may be less (often much less) than 5%.63 For some categories of modern organisms, such as the wide range of microbes, essentially no informative fossils exist at all.

Once scientists recognized that fossils provide evidence for extinct organisms, the obvious question was, do extinct organisms fit into the same cladistic classification scheme as do living organisms or do they form their own groups or their own separate trees? This can be a difficult question to answer, since many fossils are only fragments of the intact organism. The fragmentary nature of the fossil record can lead to ambiguities. Nevertheless, the conclusion that has emerged upon careful characterization is that we can place almost all fossilized organisms within the cladistic classification scheme developed for modern organisms, with a few possible exceptions, such as the Ediacarian organisms that lived very long ago and appear (perhaps) to be structurally distinct from all known living organisms.64 The presumption, however, is that if we had samples of Ediacarian organisms for molecular analyses, we would find it that they would fall nicely into the same classification scheme as all other organisms do.65 A similar example are the dinosaurs, which while extinct, are clearly descended from a specific type of reptile that also gave rise to modern birds, while mammals are more closely related to a second, now extinct group, known as the “mammal-like reptiles.”

In rare cases, particularly relevant to human evolution, one trait that can be recovered from bones is DNA sequence data. For example, it has been possible to extract and analyze DNA from the bones of Neanderthals and Denisovian-type humanoids, that went extinct about 30,000 years ago. This is information that has been used to clarify their relationship to modern humans (Homo sapiens).66 In fact, such data has been interpreted as evidence for interbreeding between these groups and has led for calls to reclassify Neanderthals and Denisovians as subspecies of Homo sapiens.

The main unifying idea in biology is Darwin’s theory of evolution through natural selection.

– John Maynard Smith


Phylogeny

VII.D. Phylogeny and Biodiversity: Phylogenetic Diversity

Phylogenies also provide a framework for alternative ways of looking at biodiversity. Most measures of biodiversity use species richness, either in a geographic (either broad or local) or ecologic sense. Other views of diversity may focus on the nature and breadth of adaptation. Such measures unfortunately require a subjective view of the importance of particular adaptations—e.g., the birds might be considered “diverse” because they include so many adaptations for use of the bill. However, phylogeny provides another perspective on biodiversity that allows an objective way to compare uniqueness and diversity of taxa. Although various specific measures of phylogenetic diversity have been proposed, most share a basic approach by which phylogenetic trees are used to evaluate species richness in concordant groups. It means little to say that “orchids are highly speciose” or “monotremes are species depauperate” unless we have some idea as to the relationships of the two groups being compared. Phylogenetic pattern provides the basis for such comparisons.

Currently, the use of phylogenetic diversity measures is largely limited to theoretical discussions and there have been few efforts to actually apply such measures to conservation. This is partly due to the relative paucity of high-quality phylogenies that are available across broad groups of taxa and partly because of a distinctly ecological bias in most studies of biodiversity. As molecular data sources provide better and more complete phylogenies for use by other workers, this is likely to change. It is probable that in the near future measures of phylogenetic diversity will become standard components, in combination with more traditional measures of ecologic uniqueness, species richness, and sensitivity, in the formulae that are used to evaluate conservation priorities for areas and endangered species.


Implications of Cladistics

The output from a phylogenetic analysis is a hypothesis of relationship of different taxa. This hypothesis can be represented as a cladogram, a branching diagram. Cladograms bear a lot in common with the notion of family trees. In a family tree we trace back our ancestry. For example, in the family tree on the right, the ancestors of all the rest of the family are the initial black dot and yellow square. These ancestors give rise to three children, one of which mates and has two children. We can all trace our lineages back to one set of ancestors.

All species have ancestors too. So, for example, sometime in the past an ancestral species (father) of Homo sapiens walked the earth. This ancestor went extinct (died), but left descendent species (children).

In family trees, we can talk coherently about real ancestors. In biology, the ancestors are often gone sometimes without a trace. All we have left are the children. Reading cladograms is much like reading a family tree. Both are rich in information. Cladograms, like family trees, tell the pattern of ancestry and descent. Unlike family trees, ancestors in cladistics ideally give rise to only two descendent species. Also unlike family trees, new species form from splitting of old species. In speciation, it does not take two to tango. The formation of the two descendent species is called a splitting event. The ancestor is usually assumed to "die" after the splitting event.

In the first tree, labelled Cladogram A, notice the small circles. These mark the nodes of the tree. The stems of the tree end with the taxa under consideration. At each node a splitting event occurs. The node therefore represents the end of the ancestral taxon, and the stems, the species that split from the ancestor. The two taxa that split from the node are called sister taxa. They are called sister taxa because they are like the siblings from the parent or ancestor. The sister taxa must each be more closely related to one another than to any other group because they share a close common ancestor. In the same way, you are most closely related to your siblings than to anyone else since you share common parents. Lets focus on node C in Cladogram A. At the node, the ancestor goes extinct but leaves two siblings hypothesized to be humans and gorillas. Humans and gorillas are sister taxa and are more closely related to one another than either is to chimpanzees or baboons.

Working down the tree we come to node B. At this node the ancestor of the humans and gorillas split from the chimpanzees. Therefore the chimpanzees sister taxon is the human/gorilla ancestor. A sister taxon can be an ancestor and all its descedents. We call an ancestor plus all its descendents a clade. A cladogram shows us hypothesized clades.

Finally we come to node A. Here, we find the splitting event that led to the baboons and the ancestor to the chimpanzees, humans and gorillas. By working our way down the cladogram we have learned the pattern of splitting. We have found out that chimpanzees, humans and gorillas are more closely related to each other than to baboons. In this example, baboons are the outgroup.

Now, how in the world did we manufacture Cladogram A? We mentioned that it was a hypothesis. What if it we chose another hypothesis like Cladogram B or Cladogram C? We would change the pattern of speciation events. In Cladogram B, humans and chimpanzees are sister taxa and in Cladogram C, chimps and gorillas are sister taxa.

Which of the three cladograms presented above is correct? None of the cladograms can be proved correct, but Cladogram B is the best supported of the three based on character data and is therefore hypothesized to best reflect the true branching pattern.

Manufacturing cladograms which show hypotheses of ancestry and descent requires that we analyze characters and find those characters that unite clades.


Molecular phylogenetics, morphological cladistics, and fossil record

Paleontological fit of different kinds of cladograms is considered using the ghost range method, the ghost range being the time gap between dates of supposed and paleontologically confirmed appearance of a taxon. The absolute and relative length of total ghost ranges in the published morphological and molecular cladograms and, in some cases, traditional (‘intuitive’) cladograms were calculated. Orders of winged insects as well as families of some of these orders were the terminal taxa of the cladograms (in all, 42 cladograms for 14 sets of terminal taxa). A new index is proposed to assess the relative amount of ghost ranges: GRI = 1-L0/LM, where L0 is the sum of ghost ranges in a particular cladogram and LM is the maximum possible sum of ghost ranges in a cladogram with the same set of terminal taxa. As in the previous studies (Rasnitsyn, 2000, 2005), calculations showed the intuitive cladograms to be clearly superior to both molecular and morphological ones in their stratigraphic fit. Another result, namely that molecular cladograms showed no advantage over morphological cladistics, was unexpected and apparently unexplainable. Additionally, the hypothesis of character devaluation resulting from computerized cladistic procedures (Rasnitsyn, 2002) was directly supported for the first time by our calculations.


Acknowledgements

We thank Catherine Kemper, David Stemmer, Neville Pledge, Mary-Anne Binnie (South Australian Museum, Adelaide, Australia) for access to collections and allowing photography during Tsai's visit Erich Fitzgerald, Nicholas Pyenson and three anonymous reviewers for constructive comments, and the handling editor Paul Sniegowski for advice Daniel Thomas, Daniel Ksepka and Felix Marx for review and comments Erich Fitzgerald and Robert Boessenecker for discussion.

Author contributions

C.-H.T. designed the research and conducted the phylogenetic analyses. C.-H.T. and R.E.F. collected data, and wrote the paper.

Funding statement

C.-H.T. was supported by a University of Otago Doctoral Scholarship.

Competing interests

Authors have declared that no competing interests exist.


How to do cladistics [ edit ]

A cladistic analysis is applied to a certain set of information. The information is organised by characters, which have character states. e.g., if one species has red feathers and another has blue feathers, then we have the character "colour of feathers" which has character states "red feathers" and "blue feathers".

The researcher decides which character states were present before the last common ancestor of the species group (plesiomorphies) and which were present in the last common ancestor (synapomorphies) by considering one or more outgroups - an organism considered not to be part of the group in question, but to be closely related to the group. (This makes the choice of an outgroup an important task, since this choice can profoundly change the topology of a tree.) Only synapomorphies are of use in determining clades.

Possible cladograms are then drawn up and evaluated. Ideally, clades have many "agreeing" synapomorphies, with a sufficient number of true synapomorphies to overwhelm homoplasies caused by convergent evolution - characters that resemble each other because of environmental conditions or function, not because of common ancestry. A character "presence of wings" is an example - though the wings of birds and insects serve the same function, each evolved independently, as can be seen by their anatomy. If a bird and a winged insect were scored for the character "presence of wings", a homoplasy would be introduced into the dataset and confound the analysis, possibly resulting in an erroneous picture of evolution. Homoplasies can often be avoided by defining characters more precisely and increasing their number, e.g., using "wings supported by bony endoskeleton" and "wings supported by chitinous exoskeleton" as characters.

When analyzing "supertrees" (datasets incorporating as many taxa of a suspected clade as possible), it may be unavoidable to introduce character definitions that are unprecise, as otherwise the characters might not apply at all to a large number of taxa. The "wings" example would be hardly useful if attempting a phylogeny of all Metazoa as most of these don't have wings at all. Cautious choice and definition of characters thus is another important element in cladistic analyses. With a faulty outgroup and/or character set, no method of evaluation is likely to produce a phylogeny representing the evolutionary reality.

Many cladograms are possible for any given set of taxa, but one is chosen based on the principle of parsimony: the most compact arrangement, that is, with the fewest character state changes (synapomorphies), is the hypothesis of relationship accept here (see Occam's razor for a discussion of the principle of parsimony and possible complications). Though at one time this analysis was done by hand, computers are now used to evaluate much larger data sets. Sophisticated software packages such PAUP allow the statistical evaluation of the confidence we can put in the veracity of the nodes of a cladogram.

Note that the nodes of cladograms do not represent divergences of evolutionary lineages per se, but divergences of character states between evolutionary lineages. DNA sequence characters can only diverge after gene flow between (sub)populations has been reduced below some threshold, whereas comprehensive morphological alterations, usually being epistatic (the product of interactions of several genes), usually occur only after lineages have already evolved separately for quite some time - biological subspecies can usually be distinguished genetically but often not by internal anatomy.

As DNA sequencing has become cheaper and easier, molecular systematics has become more popular. As well as a parsimony criterion, you can also use non-Hennigian methods such as maximum likelihood and Bayesian inference, which incorporate explicit models of sequence evolution. Another powerful method is the use of genomic retrotransposon markers, which are thought to be less prone to the problem of reversion that plagues sequence data. They are also generally assumed to have a low incidence of homoplasies because it was once thought that their integration into the genome was entirely random, although it now appears that this is sometimes not the case.

Ideally, morphological, molecular and possibly other (behavioral etc.) phylogenies should be combined into an analysis of total evidence: none of the methods is "superior", but all have different intrinsic sources of error. For example, character convergence (homoplasy) is much more common in morphological data than in molecular sequence data, but character state reversions that cannot be noticed as being such are more common in the DNA. Morphological homoplasies can usually be recognized as such if character states are defined with enough attention to detail.


Understanding Cladistics

At the American Museum of Natural History, scientists use a method called cladistics to group animals. They look for unique features, such as a hole in the hip socket, that the animals share. Animals with like features are grouped together. A chart, called a cladogram, shows these relationships. Using cladistics, scientists can reconstruct genealogical relationships and can show how animals are linked to one another through a long and complex history of evolutionary changes.

Objective

In this activity, students will explore cladistics and create a cladogram of their own.

  • A penny, nickel, dime, and quarter for each pair of students
  • 6-8 dinosaurs pictures duplicated for each group, downloadable from amnh.org/resources/rfl/pdf/dino_16_illustrations.pdf
  • Procedure

1. Write lion, elephant, zebra, kangaroo, koala, buffalo, raccoon, and alligator. Ask students how the animals are related and what might be a good way of grouping them into sets and subsets. Discuss students responses.

2. Explain to students that scientists use a method called cladistics to determine evolutionary relationships among animals. They look for features that animals share, such as four limbs, hooves, or a hole in the hip socket. Animals with like features are grouped together. Scientists make a chart called a cladogram to show these relationships.

3. Tell students that they will examine the features of various coins to determine how they are related. Remind students that cladistics is used to determine relationships among organisms, and not necessarily objects. The exercise they are about to do will introduce them to how cladistics works. Have students work in pairs. Distribute Understanding Cladistics to students. Have them complete the activity and compare their cladograms. Discuss how they arrived at their conclusions and any differences among the cladograms.

4. Duplicate and distribute illustrations of six to eight dinosaurs. Ask students to work in groups to classify the dinosaurs according to features they identify. Have groups share their findings.


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Enzymes 2.502 Molecular biology

Enzymes control almost everything which happens inside the cells of all living organisms. In this topic we consider how enzymes make reactions faster as well as the effects of different environmental factors on the rate of enzyme controlled reactions.

&hellips yourself from memory. Gallery: MM Enzymes 2.5 Mode: carousel Thumb width: 48px Layout: row Test yourself - multiple choice questions This is a self marking quiz containing questions covering the topic outlined above. Try the questions to check your&hellip

Inheritance 10.2 HL10 Genetics AHL

Inheritance has been covered in the SL genetics topic already so this HL topic covers dihybrid crosses and the discovery of linkage by Morgan with Drosophila flies. The prediction of phenotype ratios and recognition of recombinant phenotypes is required.

&hellipps from memory. Gallery: MM Inheritance HL 10.2 Mode: carousel Thumb width: 48px Layout: row Test yourself - multiple choice questions This is a self marking quiz containing questions covering the topic outlined above. Try the questions to check your&hellip

Carbon Cycle 4.3 04 Ecology

The processes of the carbon cycle include photosynthesis and respiration. This topic gets tricky in other connected aspects of the global carbon cycle. These include storage of carbon containing molecules in peat, fossil fuels, coral, and the oceans.

&hellipmemory if you can. Gallery: MM Carbon cycle 4.3 Mode: carousel Thumb width: 48px Layout: row Test yourself - multiple choice questions This is a self marking quiz containing questions covering the topic outlined above. Try the questions to check your&hellip

Movement 11.2 HL11 Animal physiology AHL

This topic covers the basic structure of joints and the role of bones and exoskeletons in movement before looking in detail at the structure of sarcomeres in skeletal muscles and the processes of the sliding filament theory.

&helliplike these concept maps from memory. Gallery: MM Movement 11.2 Mode: carousel Thumb width: 48px Layout: row text Exam style questions Sarcomere structure Understanding the structure of sarcomeres and their dark and light bands is an important skill&hellip

Sexual reproduction 11.4 HL11 Animal physiology AHL

Sexual reproduction in this HL topic begins with spermatogenesis and oogenesis where gametes are made. This is followed by the process of fertilisation, the acrosome reaction and the cortical reaction. The development and implantation of a blastocyst.

&hellipr concept map from memory. Gallery: MM Sexual reproduction 11.4 Mode: carousel Thumb width: 48px Layout: row text Exam style questions Sexual reproduction Understanding the structure of mature sperm cells and the placenta are both important steps in&hellip

Transport in xylem 9.1 HL09 Plant biology AHL

This topic relies on a knowledge of the structure of the leaf, its air spaces and stomata. The transport of water through a plant is driven by transpiration in leaves. Water evaporates from the surfaces of cells and this water vapour fills the air spaces.

&hellipfrom memory. Gallery: MM Transport in xylem 9.1 Mode: carousel Thumb width: 48px Layout: row Test yourself - multiple choice questions This is a self marking quiz containing questions covering the topic outlined above. Try the questions to check your&hellip

Inheritance 3.403 Genetics SL

Theoretical genetics started with Gregor Mendel who established some simple rules of inheritance based on the idea that characteristics or "traits" are inherited independently. The gametes carry a single copy of any gene which becomes a pair of alleles.

&hellipmemory if you can. Gallery: MM Inheritance 3.4 Mode: carousel Thumb width: 48px Layout: row Test yourself - multiple choice questions A quiz containing multiple choice questions covering the understanding and skills from this topic. 3.4 Inheritance&hellip

Energy flow 4.204 Ecology

The transfer of energy within food webs. This topic is all about the way that energy from sunlight is trapped by photosynthesis and then passed from organism to organism in a food web.

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Hormones and reproduction 6.606 Human physiology

Learn about homeostasis, thermoregulation, control of blood glucose, diabetes, leptin, melatonin, male and female reproductive systems, the SRY gene, secondary sexual characteristics and the menstrual cycle.

&helliprom memory. Gallery: MM Hormones and reprod 6.6 Mode: carousel Thumb width: 48px Layout: row Test yourself - multiple choice questions This is a self marking quiz containing questions covering the topic outlined above. Try the questions to check your&hellip

Gas exchange 6.406 Human physiology

Learn about the difference between the ventilation system and gaseous exchange. This topic covers the functions of parts of the lung, the mechanism of inspiration, expiration and the structure of the alveolus.

&hellipmaps from memory. Gallery: MM Gas exchange 6.4 Mode: carousel Thumb width: 48px Layout: row Test yourself - multiple choice questions A quiz containing at least ten questions covering the ten skills outlined in the image above. 6.4 Gas exchange quiz&hellip

Chromosomes 3.203 Genetics SL

Chromosomes are circular in prokaryotes and linear in eukaryotes. The number of chromosomes is a characteristic of eukaryote species. The structure and shape of the chromosomes in an organism can also give information about the genetic diseases and gender.

&hellipmemory if you can. Gallery: MM Chromosomes 3.2 Mode: carousel Thumb width: 48px Layout: row Test yourself - multiple choice questions A quiz containing multiple choice questions covering the understanding and skills from this topic. 3.2 Chromosomes&hellip

Genes 3.1 03 Genetics SL

Genes provide the instructions to build proteins and more besides. The human genome has been decoded by the human genome project and now biologists can search databases to find the location of specific genes.

&hellip, from memory if you can. Gallery: MM Genes 3.1 Mode: carousel Thumb width: 48px Layout: row Test yourself - multiple choice questions A quiz containing multiple choice questions covering the understanding and skills outlined in the image above. 3.1&hellip


From Haeckel’s phylogenetics and Hennig’s cladistics to the method of maximum likelihood: Advantages and limitations of modern and traditional approaches to phylogeny reconstruction

The maximum likelihood and Bayesian methods are based on parametric models of character evolution. They assume that if we know these models as well as distribution of character states in studied organisms, we can infer the probability of different phylogenetic trajectories leading from ancestors to modern forms. In fact, these methods are mathematized variants of the traditional Haeckel’s approach to phylogeny reconstruction. In contrast to classical and parsimonious cladistics, they infer phylogenies without such limitations as necessity of strictly dichotomous evolution, exclusion of plesiomorphic characters, and acceptance of only holophyletic taxa. They assume that evolution may be reticulated, any homologous characters—both apomorphic and plesiomorphic—can be used for inferring phylogenies, and interpretation of evolutionary lineages as taxa is optional. Thus, the main difference between the new and more traditional approaches to phylogeny reconstruction lies not in the characters used (molecular or morphological) but in the methodology of analysis. It must be admitted that a revolution began in phylogenetics 10–20 years ago. However, the fundamental changes in phylogenetics have been carried out so calmly and neatly by the people who started this revolution, that many systematists still do not realize their importance.


Introduction to the Lophotrochozoa

The Lophotrochozoa comprise one of the major groups within the animal kingdom, In turn, the Lophotrochozoa belongs to a larger group within the Animalia called the Bilateria, because they are bilaterally symmetrical with a left and a right side to their bodies.

The cladogram above shows the major groups in the Lophotrochozoa. Click on any box containing a picture to learn about that particular group. The phylogeny above is based on a combination of morphology and 18S RNA. It is not the final word on the relationships between these groups, and there are many competing hypotheses. For now, we prefer this grouping based on the available evidence, but as data continues to accumulate our picture of the relationships may change.

The name Lophotrochozoa comes from the names of the two major animal groups included: the Lophophorata and the Trochozoa. In the cladogram above, you can see this division. Those animals to the left side of the cladogram are the Lophophorata, while the groups along the top and right side (Nemertini through Annelida) belong to the Trochozoa.

Trochozoa: These animals are all protostomes -- the mouth develops before the anus in the young embryo -- and they have long been recognized as belonging together as a group. Many of the members are worm-like, though not all of them are familiar or common. The two largest groups of trochozoans are the Mollusca (molluscs) and the Annelida (segmented worms).

It might seem strange at first to group earthworms and squid together. They certainly don't look much alike, but that is only true when looking at the adult form there is a fundamental feature of their life history that they share. Many annelids and molluscs share patterns of development in early embryonic stages. When these larvae hatch, each is a microscopic swimmer known as a trochophore larva, shown at right. The larva has two bands of cilia around the middle that are used for swimming and for gathering food, and at the "top" is a cluster of longer flagellae. So the larvae of these groups is nearly identical, even though they mature into very different adult forms. Until very recently, the Arthropoda (insects & crustaceans) were considered possible close relatives of the Annelida, based on the fact that both groups are segmented, but no arthropod has a trochophore larva and no molecular studies support a close relationship.

Lophophorata: This group includes the Phoronida and Entoprocta (both small groups) as well as the Bryozoa ("moss" animals) and Brachiopoda (brachiopods), both of which have an extensive fossil record. The feature shared by this group is the lophophore, an unusual feeding appendage bearing hollow tentacles.

While the Lophophorata are a well-recognized group, phylogenetic studies do not yet agree on the identity of their closest relatives. These animals were once included in the Pseudocoelomata, because they do not have a distinct internal body cavity like the Trochozoa, but this grouping does not hold together in modern studies. We have placed the Lophophorata in the Lophotrochozoa as the most popular of the current choices in the literature, but there are studies that suggest they may belong with the deuterostomes, or may even be paraphyletic.


Watch the video: Ένζυμα - βιολογικοί καταλύτες (January 2022).