Molecular characters can include differences in the amino-acid sequence of a protein, differences in the individual nucleotide sequence of a gene, or differences in the arrangements of genes. Phylogenies based on molecular characters assume that the more similar the sequences are in two organisms, the more closely related they are. Different genes change evolutionarily at different rates and this affects the level at which they are useful at identifying relationships. Rapidly evolving sequences are useful for determining the relationships among closely related species.
More slowly evolving sequences are useful for determining the relationships between distantly related species. To determine the relationships between very different species such as Eukarya and Archaea, the genes used must be very ancient, slowly evolving genes that are present in both groups, such as the genes for ribosomal RNA.
Comparing phylogenetic trees using different sequences and finding them similar helps to build confidence in the inferred relationships. Sometimes two segments of DNA in distantly related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not.
For example, the fruit fly shares 60 percent of its DNA with humans. Why Does Phylogeny Matter? In addition to enhancing our understanding of the evolutionary history of species, our own included, phylogenetic analysis has numerous practical applications.
Two of those applications include understanding the evolution and transmission of disease and making decisions about conservation efforts. A study 3 of MRSA methicillin-resistant Staphylococcus aureus , an antibiotic resistant pathogenic bacterium, traced the origin and spread of the strain throughout the past 40 years. The study uncovered the timing and patterns in which the resistant strain moved from its point of origin in Europe to centers of infection and evolution in South America, Asia, North America, and Australasia.
The study suggested that introductions of the bacteria to new populations occurred very few times, perhaps only once, and then spread from that limited number of individuals. This is in contrast to the possibility that many individuals had carried the bacteria from one place to another. This result suggests that public health officials should concentrate on quickly identifying the contacts of individuals infected with a new strain of bacteria to control its spread. A second area of usefulness for phylogenetic analysis is in conservation.
Biologists have argued that it is important to protect species throughout a phylogenetic tree rather than just those from one branch of the tree. Doing this will preserve more of the variation produced by evolution.
For example, conservation efforts should focus on a single species without sister species rather than another species that has a cluster of close sister species that recently evolved. If the single evolutionarily distinct species goes extinct a disproportionate amount of variation from the tree will be lost compared to one species in the cluster of closely related species.
A study published in 4 made recommendations for conservation of mammal species worldwide based on how evolutionarily distinct and at risk of extinction they are. The study found that their recommendations differed from priorities based on simply the level of extinction threat to the species.
The study recommended protecting some threatened and valued large mammals such as the orangutans, the giant and lesser pandas, and the African and Asian elephants. But they also found that some much lesser known species should be protected based on how evolutionary distinct they are. These include a number of rodents, bats, shrews and hedgehogs. In addition there are some critically endangered species that did not rate as very important in evolutionary distinctiveness including species of deer mice and gerbils.
While many criteria affect conservation decisions, preserving phylogenetic diversity provides an objective way to protect the full range of diversity generated by evolution.
How do scientists construct phylogenetic trees? Presently, the most accepted method for constructing phylogenetic trees is a method called cladistics. This method sorts organisms into clades , groups of organisms that are most closely related to each other and the ancestor from which they descended.
For example, in [Figure 4] , all of the organisms in the shaded region evolved from a single ancestor that had amniotic eggs. Consequently, all of these organisms also have amniotic eggs and make a single clade, also called a monophyletic group. Clades must include the ancestral species and all of the descendants from a branch point. Which animals in this figure belong to a clade that includes animals with hair?
Which evolved first: hair or the amniotic egg? The amniotic egg evolved before hair, because the Amniota clade branches off earlier than the clade that encompasses animals with hair.
Clades can vary in size depending on which branch point is being referenced. The important factor is that all of the organisms in the clade or monophyletic group stem from a single point on the tree. Cladistics rests on three assumptions. The first is that living things are related by descent from a common ancestor, which is a general assumption of evolution.
The second is that speciation occurs by splits of one species into two, never more than two at a time, and essentially at one point in time. This is somewhat controversial, but is acceptable to most biologists as a simplification.
The third assumption is that traits change enough over time to be considered to be in a different state. It is also assumed that one can identify the actual direction of change for a state. In other words, we assume that an amniotic egg is a later character state than non-amniotic eggs.
The human arm is composed of the same set of bones, i. They are examples of homologous structures. Although their forelimbs are used differently, the basic skeletal structure is the same and they are derived from the same embryonic origin.
This holds true as well to the lower limbs of animals when the basic bone components include femur, tibia, and fibula. In this regard, animal limbs lacking bones like those of starfish and insects will, therefore, be not homologous to the limbs of the animals that contain bone structures as depicted above.
Vestigial structures are another example. They are remnants of the ancestral form. Over time, these structures could eventually lose or alter the original function. Nevertheless, they are essential as they could provide a clue or evidence as to the evolutionary history of a species. For example, the snake has remnants of a pelvis. This structure is homologous to the pelvises of humans, dogs, and cats.
Humans have vestigial structures, too. The human tailbone palpable during the embryonic stage is a shred of evidence that humans and other tailed-mammals do share a common ancestor. It should be pointed out though that one should not be too quick to think that all similarity is homology. Evolution has reduced their size because the structures are no longer used. The human appendix is another example of a vestigial structure. It is a tiny remnant of a once-larger organ. In a distant ancestor, it was needed to digest food.
It serves no purpose in humans today. Why do you think structures that are no longer used shrink in size? Darwin could compare only the anatomy and embryos of living things. Today, scientists can compare their DNA. Similar DNA sequences are the strongest evidence for evolution from a common ancestor. More similarities in the DNA sequence is evidence for a closer evolutionary relationship.
Look at the cladogram in the Figure below. It shows how humans and apes are related based on their DNA sequences. Cladogram of Humans and Apes. This cladogram is based on DNA comparisons. It shows how humans are related to apes by descent from common ancestors. In search of the common ancestor of all mammals, University of California Santa Cruz scientist David Haussler is pulling a complete reversal.
Instead of studying fossils , he's comparing the genomes of living mammals to construct a map of our common ancestors' DNA. He also specializes in studying the DNA of extinct animals, asking how the DNA has changed over millions of years to create today's species.
His technique, referred to as computational genomics, holds promise for providing a better picture of how life evolved. Comparative Anatomy Comparative anatomy is the study of the similarities and differences in the structures of different species.
The forelimbs of all mammals have the same basic bone structure. Comparative Embryology Comparative embryology is the study of the similarities and differences in the embryos of different species. Vestigial Structures Structures like the human tail bone and whale pelvis are called vestigial structures.
Comparing DNA Darwin could compare only the anatomy and embryos of living things. Summary Scientists compare the anatomy, embryos, and DNA of living things to understand how they evolved.
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