Applied Phylogenetics - Lab Report Example

Applied Phylogenetics Lab Report Introduction Evolutionary relationships among various groups can be depicted using a cladogram, which can be produced using either of three characteristics that are genes, proteins, and morphology. However, this diagram cannot be considered as an evolutionary tree since it fails to show the relation between ancestors and descendants or the manner in which they have changed, although one can infer numerous evolutionary trees from one diagram (Purvis et al 22). The diagram uses branching lines that end at specific groups of organism and the lines branch off into separate directions. Despite the shape of any cladogram, they all have branching lines from one another, which can be traced back to the point they branched from. The points at which the branching off occurs indicates the presence of hypothetical ancestors, rather than actual ancestor entities, which possess the combined traits of lines on top of it. It is then possible to give clues from the hypothetical ancestor about what may be present in a real evolutionary ancestor. While morphology was traditionally used to generate cladograms, computational phylogenetics and sequencing of genetic data and gene products (proteins) data are now the most common means of producing cladograms (Purvis et al 23). For this lab session, molecular and morphological cladograms were created for five different species, and another molecular cladogram created for 5 different subspecies of the American black bear. Results In the cladogram for five different species using molecular data, the Virginia opossum has the least similarity in sequence with the other species, while its mitochondrial DNA shows little variability. It was also the first of these species to evolve followed by the domestic horse, which shows only 3% sequence similarity with the other species. The white tailed deer shows no sequence similarity with the other species and within the species there is variability in mitochondrial DNA of 61%. The domestic dog has 2% sequence similarity and no mitochondrial DNA variability. With regards to the cladogram on five species using morphological data, the fish is the outlier group and has the least in common with the other species. The duck and the humming bird are the two most closely related species, while the mouse and bat also share a close ancestor, although the mouse has evolved further than the bat. Finally, regarding the cladogram of the American black bear, Ursus americanus cinnamomum shares the least similarity in mitochondrial DNA sequence followed by Ursus americanus americanus. Ursus americanus kermodei has the least sequence similarity among the rest. Discussion Protection of biological diversity can be defined on the basis cladogram information analysis. For this lab report, an examination of the null hypothesis was done through interpretation of cladograms. In the cladogram for five species of mammals, including the domestic dog, the Virginia opossum, domestic horse, white-tailed deer, and domestic cat, information was derived from their molecular data. The cladogram rejected the null hypothesis because the species did display a distribution of their derived molecular states. With regards to the cladogram on the six subspecies of American black bear, constructed using the mitochondrial DNA, after which the results were interpreted on the basis of the null hypothesis regarding the evolution of the black bear subspecies during glaciations in the past. The null hypothesis in this case was also rejected, supporting the prior hypothesis that large islands acted as a refuge for subspecies of these bears. Finally, the null hypothesis for the cladogram based on morphological features for five different species was also rejected because the different species show that they display derived character state distribution. Protection of biologically ancient network areas, of which estimation is done by branch length; on the cladogram constructed using mitochondrial DNA is more efficient because the networks are more representative of maximum phylogenetic diversity and overall phylogenetic diversity. In constructing these cladograms, three methods were used with basis on morphological, protein, and genetic characteristics. Cladograms constructed using morphological characteristics have several advantages, such as the ease of morphology observation without harming or even handling the animal, while it is also easy to communicate results to many people who understand morphology (Wiley & Lieberman 34). However, it also has several disadvantages, including the fact that morphology variation in fossil records may be too vast, while there is a possibility that two species may be similar morphologically but distinct genetically. In addition, it relies on interpretation by humans in definition of species instead of natural mechanisms. The genetics methodology has several advantages, such as providing independent evidence for both biological and morphological species, saves time for small organisms and bacteria, and enhances the ability to attain more samples from a single individual (Wiley & Lieberman 45). Disadvantages of this methodology is that it is also reliant on human judgment in determining if the differences constitute a separate species, while taking of DNA is invasive and raises the risk of DNA contamination. Finally, communicating DNA taxonomy to non-specialists may be difficult. With regards to protein methodology, its advantages include the fact that analysis can be done by hand, additional data can be added to evolutionary trees without recalculating distance matrices, and qualitative output defines states of character for all branches on the tree, affording a high testability degree (Wiley & Lieberman 61). However, it could also present too many alternative trees for a specific set of data. American black bears once lived all over North America and were driven into forested areas by agriculture and hunting. Today, residual populations have survived in woodlands that are sparsely populated over much of the subspecies range, as well as in protected national parks. While they are still thriving and numerous, they still face regional threats because of hunting and habitat destruction. The Louisiana black bear, which is one of the black bear subspecies; however, is listed as endangered because of habitat fragmentation and loss, while there is evidence that the subspecies could have interbred with Minnesota black bears, resulting in poor distinguishing ability between the two subspecies (Wiley & Lieberman 102). This is good example of species loss since the Louisiana black bear could lose its position as a species. In addition, heterozygosity has also impacted on black bears. Their body cells normally carry two alleles for a specific genetic trait. If the cells contain two similar alleles for a specific trait, also known as homozygosity, they will express that trait be it recessive or dominant. Loss of heterozygosity in the Kermode black bear subspecies has resulted in their white fur because they have two recessive alleles that are expressed because of a mutation. The only way that this fur colour can be expressed is through loss of heterozygosity, causing the presence of two white alleles that are recessive (Wiley & Lieberman 103). Therefore, the Kermode subspecies is homozygous recessive for colour of its fur and their cells express proteins for white fur. With the current crisis regarding biodiversity globally, and especially in North America, scientists are required to develop ways for strategic allocation of conservation efforts. One of the proposals that have received support is the direct integration of evolutionary relationships between phylogenies into biodiversity conservation priority definitions (Höglund 45). Phylogenetic approaches have especially become vital in conservation in the last twenty years with the importance of preserving phylogenetic diversity becoming critical. This is because species that are more phylogenetically diverse are able to maintain higher and stronger function. In fact, it has been opined that phylogenetic diversity is able to explain the productivity of species better than many other diversity measures. Moreover, it has also been proven that phylogenetic diversity is crucial in enhancing the stability of a particular ecosystem. In this case, ground biomass production shows increased stability in communities that are made up of species with distant relationships. By matching results collected from communities of organisms, organism communities that are more diverse phylogenetically tend to show increased productivity (Höglund 46). However, if these same organisms are allowed to reproduce and evolve in another new environment, there is a perceptible weakening in this relationship, which can be explained by a loss of adaptation. Therefore, understanding mechanisms of evolution will be of help since it allows the use of phylogenetic diversity as an ecosystem functioning proxy. In spite of the small number of American black bear subspecies, phylogenetics has been a long-term focus because of its potential value in conservation, while most members of the bear genera are classified as endangered at subspecies level (Höglund 71). As part of the Ursidae family, American black bears are a good example of rapid radiation in evolution with previous analysis using a small mitochondrial gene amount or a single mitochondrial gene providing huge polytomy that is unresolved for ursids. By analyzing the complete sequences of mitochondrial genome, while also evaluating constituent mitochondrial DNA genes and entire mitochondrial genes to recover the phylogeny of very recent events of speciation, it is possible to pinpoint a member of the American black bear species that requires conservation. Identifying base composition utilization and bias of the data that has been combined for entire sequences of mitochondrial genome will allow for the recovery of phylogeny that has strong support. This can be upheld through the use of multiple and alternative black bear out-groups, which underwent rapid radiation and some of them, may be threatened with extinction (Höglund 73). Therefore, by providing a robust phylogenetic framework for the American black bear subspecies, conservationists can use them for future validation since they produce independent evidence to assist in the resolution of subspecies that have strayed too far from the evolutionary tree and, thus, may be threatened with extinction. Staying with conservation, phylogenetics can aid in the study of subspecies susceptibility and threat factors. The value of conservation in a locality is dependent on additional components that it can add to biodiversity, rather than those already present (Purvis et al 67). The key to accounting for the value of biodiversity of certain locations lies in consideration of range sizes held by the subspecies. Information from phylogenetic analysis is becoming widely recognized as a way to evaluate priorities for conservation, although associations between susceptibility to extinction and phylogenic properties like rates of diversification and lineage ages for phylogeny are still not clear. Susceptibility risks increase for subspecies that are evolutionarily distinctive, while decreasing with lineage age when some subspecies are excluded (Purvis et al 69). Subspecies that have more close relatives tend to be less threatened than those that have drifted too far from the evolutionary tree. Works Cited Höglund, Jacob. Evolutionary Conservation Genetics. Oxford: Oxford University Press, 2009. Print. Purvis, Andy. Gittleman, John. L. & Brooks, Thomas. Phylogeny and Conservation. Cambridge: Cambridge University Press, 2005. Print. Wiley, Edward. & Lieberman, Bruce. S. Phylogenetics: Theory and Practice of Phylogenetics Systematics. Hoboken, N.J: Wiley-Blackwell, 2011. Print. Read More