A 3.2.4 - A 3.2.6 Clades & Molecular Clocks PDF

ATHIF SYAK ADIB KHAI  A3.2.4 CLADES DISPLAY COMMON ANCESTRIES AND SHARED CHARACTERISTICS The most objective evidence for placing organisms in the same clade comes from base sequences of genes or amino acid sequences of proteins. Morphological traits can be used to assign organ...

ATHIF SYAK ADIB KHAI  A3.2.4 CLADES DISPLAY COMMON ANCESTRIES AND SHARED CHARACTERISTICS The most objective evidence for placing organisms in the same clade comes from base sequences of genes or amino acid sequences of proteins. Morphological traits can be used to assign organisms to clades.  Clades Cladistics Cladogram a system of a group of organisms a diagram illustrating classification for that includes a single evolutionary grouping taxa based ancestor and all of its relationships between on the characteristics descendents. species. Also called as have evolved most phylogenetic tree recently clades can be very large & include thousands of species or can be very small with just a few of species every species in a multiple clades smaller clades are “nested” within larger clades  primitive plesiomorphic characteristics that have a similar structure and function (e.g. leaves, with vascular tissue to transport liquids around a plant) and evolved early in the history of the organisms being studied. derived also characteristics that have similar structure and function but have evolved more recently, in the form of modifications of a previous trait (eg. apomorphic flowers, which, according to the fossil record, evolved more recently than leaves with vascular tissue). A3.2.5 GRADUAL ACCUMULATION OF SEQUENCE DIFFERENCES AS THE BASIS FOR ESTIMATES OF WHEN CLADES DIVERGED FROM A COMMON ANCESTOR This method of estimating times is known as the “molecular clock”. The molecular clock can only give estimates because mutation rates are affected by the length of the generation time, the size of a population, the intensity of selective pressure and other factors. Evidence for which species are part of a clade can be obtained from the base sequences of a gene or the corresponding amino acid sequence of a protein. Sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor. Rate of change of base sequence Mutations in DNA that persist and are inherited occur at a predictable rate example: mitochondrial DNA from humans and primates has been completely sequenced and used to construct cladogram between them The rate at which mutation occur at can be used as a molecular clock to calculate how long ago species diverged If the DNA base sequences or two species are similar......then few mutations have occurred... therefore the species only diverged relatively recently The length of the line separating species on cladograms is often used to represent the estimated time since they diverged The closest relatives of humans are chimpanzees and bonobos. The entire genome of these three species has been sequenced giving very strong evidence for the construction of a cladogram. What is molecular clock? Molecular clock is a method used to estimate divergence times based on accumulated sequence differences (mutations) in DNA or proteins. The assumption is that mutations occur at a roughly constant rate over time. Limitations of Molecular Clock Variable Mutation Rates In reality, mutation rates can vary significantly Factors influencing mutation rates include the length of the generation time (how quickly generations pass), population size, and selective pressures. For instance, species with longer generation times tend to accumulate more mutations over time. Population-Specific Factors Different species experience distinct ecological contexts, which affect mutation rates. Isolated populations may have unique genetic dynamics, leading to variations in mutation rates. Therefore, applying a universal mutation rate across all species can be oversimplified. Selective Pressure Intense selective pressure can alter mutation rates. When a species faces strong environmental challenges (e.g., predators, climate changes), mutations may occur more rapidly. Conversely, stable environments may lead to slower mutation rates. Assumptions and Estimates The molecular clock provides estimates, not precise values. Scientists assume a specific mutation rate (e.g., 10⁻⁹ mutations per year) to calculate divergence times. These estimates are valuable for understanding evolutionary timelines but should be interpreted cautiously. A3.2.6 Base sequences of genes or amino acid sequences of proteins as the basis for constructing cladograms Examples can be simple and based on sample data to illustrate the tool. NOS: Students should recognize that different criteria for judgement can lead to different hypotheses. Here, parsimony analysis is used to select the most probable cladogram, in which observed sequence variation between clades is accounted for with the smallest number of sequence changes.  By comparing base sequences, it is possible to estimate how long ago pairs of species diverged. These estimates can then be used to suggest the order in which the divergences occurred. Much more sophisticated analysis can be done using computer software. Sequences for all species in a clade can be compared in combination The software can then use calculations to determine how the species could have evolved with the smallest number of sequence changes. This is known as the parsimony criterion. It does not prove how a clade evolved but it indicates the most probable pattern of divergence. Sequence analysis is used to construct a cladogram. A cladogram is a branching diagram that represents ancestor–descendant relationships. Use of amino acid sequence of proteins in constructing cladograms Use immunological studies - as an example (Hodder Textbook) Cladograms can be constructed using amino acid sequences of proteins. An example comes from immunological studies – a means of detecting differences in specific proteins of species and, therefore (indirectly), their genetic relatedness. Typically, a rabbit is used when investigating relatedness to humans. In the rabbit, the injected serum causes the production of antibodies against the human proteins. Then, serum produced from the rabbit’s blood (now containing antibodies against human proteins) can be tested against serum from a range of animals. The more closely related a test animal is to humans, the greater the reaction of rabbit antibodies with human-like antigens The precipitation produced by the reaction of treated rabbit serum with human serum is taken as 100%. For each species tested, the greater the precipitation, the more recently the species shared a common ancestor with humans. This technique, called comparative serology, has been used by taxonomists to establish phylogenetic links in mammals and in invertebrates. Of course, we do not know the common ancestor to these animals and the blood of that ancestor is not available to test. However, if the sequence of the 584 amino acids that make up the blood protein albumin changes at a constant rate, the percentage immunological ‘distance’ between humans and any of these animals will be a sum of the distance ‘back’ to the common ancestor plus the difference ‘forward’ to the listed animal. Hence, the difference between a listed animal and human can be halved to estimate the difference between a modern form and the common ancestor The divergent evolution of the primates is known from geological (fossil) evidence. So, the forward rate of change since the lemur gives us the rate of the molecular clock – namely 35% in 60 million years, or 0.6% every million years.