Tuesday, November 29, 2022

What Is Phylogeny In Biology

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A Few Key Lines Of Supporting Evidence:

What is the Evidence for Evolution?
  • geological and fossil record, showing that the Earth is about 4.5 billion years old, and sequential changes in the kinds and forms of living organisms over geological time scales
  • homologies in body plans, structures, and DNA sequences indicative of common ancestry
  • a common biochemistry for all life on Earth the same amino acids, the same biological building blocks, the same genetic code
  • inference of evolutionary relationships from gene sequence comparisons largely agree with the fossil record, and are consistent with a common origin for all extant life on Earth.

Read And Analyze A Phylogenetic Tree That Documents Evolutionary Relationships

In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of an organism, such as from which organisms it is thought to have evolved, to which species it is most closely related, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.

Evolution Is A Theory Not Just A Hypothesis

Darwin published his theory of evolution in the Origin of Species , with carefully reasoned evidence to support this theory that all life on earth evolved from a common ancestor. This theory has been tested in numerous ways by the work of many thousands of scientists. Every test has produced results that are consistent with the theory. Evolutionary biologists conduct research to elaborate or refine the theory and understand the mechanisms at work in specific populations. Evolutionary theory now forms a framework for biological thinking, so that one famous evolutionary biologist wrote that Nothing in Biology Makes Sense Except in the Light of Evolution .The scientific use of the word theory is very different from the casual, every-day use. A scientific theory is an overarching, unifying explanation of phenomena that is well supported by multiple, independent lines of evidence i.e., composed of hundreds or thousands of independent, well-supported hypotheses. For example, germ theory is the theory that explains how microorganisms cause disease, and cell theory explains how cells function as the basic unit of life.

Title page of Darwins The Origin of Species, 1859 from Wikipedia

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Application Of Phylogenetics In Cancer Studies

Cancer research is considered one of the most significant areas in the medical community. Mutations in genomic sequences are responsible for cancer development and increased aggressiveness in patients . The combination of all such genes mutations, or progression pathways, across a population can be summarized in a phylogeny describing the different evolutionary pathways . Application of the phylogenetic tree can be explored for finding similarities among breast cancer subtypes based on gene data . Discovery of genes associated in cancer subtype help researchers to map different pathways to classify cancer subtypes according to their mutations. Methods of phylogenetic tree inference have proliferated in cancer genome studies such as breast cancer . Phylogenetic can capture important mutational events among different cancer types a network approach can also capture tumour similarities.

It has been observed from the literature that in cancer disease, the driver genes change the cancer progression, and it even affects the participation of other genes thus generating gene interaction network. Phylogenetic methods can solve the problem of class prediction by using a classification tree. Phylogenetic methods give us a deeper understanding of biological heterogeneity among cancer subtype.

Difference Between Ontogeny And Phylogeny

EVOLUTION LINK Examine the cladogram in Figure 30

Ontogeny refers to the development of an organism while phylogeny refers to how the organisms have evolved.

Let us take an example of a chicken, the ontogeny will explain the entire development cycle of the chicken right from the single cell.

Now if we consider the example of an ostrich and assume that it descended from the family of chickens, phylogeny will explain how the chicken evolved into an ostrich, i.e., it will explain the evolutionary process.

For more information on Phylogeny and other related topics, visit website or download BYJUS app for further reference.

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Impacts On Phylogenetic Inference

The reticulation and genealogical discordance generated byhybridization, HGT, ILS, and other complexities stemming from thestructure and processes involving biological lineages have,historically, been obscured by idealizing assumptions inphylogenetics. In many cases treating phylogenetic trees as idealizedmodels of genealogical history is useful and appropriate for theresearch question at hand.Figure 1 offers a good example of this. This reflects how the level ofresolution relative to our research questions can drive the way we usephylogenetic tools .

But what happens when these idealizing assumptions are criticallyinterrogated? First, the fact that different entities have different,often incompatible, genealogical histories brings into question thevery nature of phylogeny. One line of thought is that a phylogenyshould directly track genetic history rather than the history ofspeciation. As Maddison puts it,

one possible interpretation of a species phylogeny is that it depictsthe lines by which genetic information was passed on and nothingmore.

Baum and Shaw , Baum , and Velasco representa series of papers devoted to developing this concordancetree idea. Baum incorporates this line of thought aboutphylogenetic history into the debate over the nature of species andother taxa.

Limitations Of Phylogenetic Trees

It may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly varied surroundings or after the evolution of a major new adaptation, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree in Figure 4 shows that lizards and rabbits both have amniotic eggs, whereas frogs do not yet lizards and frogs appear more similar than lizards and rabbits.

Figure 4. This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share.

So, for the organisms in Figure 4, just because a vertebral column evolved does not mean that invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more phenotypically similar to each other than to a close relative.

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How To Read An Evolutionary Tree

Finally, it’s important to note that in someinstances, rectangular phylogenetic trees are drawn so that branch lengths aremeaningful. These trees are often called phylograms, and they generally depicteither the amount of evolution occurring in a particular gene sequence or theestimated duration of branches. Usually, the context of such trees makes itclear that the branch lengths have meaning. However, when this is not the case,it is important to avoid reading in any temporal information that is not shown.For example, Figure 8 may appear to suggest that the node markingthe last split leading to tips A and B occurred after the node separating tip C from tips D and E. However, this should notbe read into the tree in reality, node xcould have occurred either before or after node y.

The Taxonomic Classification System

Phylogenetic trees | Evolution | Khan Academy

Taxonomy is the science of classifying organisms to construct internationally shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then finally a single product. This organization from larger to smaller, more specific categories is called a hierarchical system.

The taxonomic classification system uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. For example, after the common beginning of all life, scientists divide organisms into three large categories called a domain: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species .

Figure 5. The taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories. The common dog, Canis lupus familiaris, is a subspecies of Canis lupus, which also includes the wolf and dingo.

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Common Misconceptions About Evolution

Here are corrections to some common misconceptions about evolution by natural selection:

  • The individual undergoing natural selection does not evolveit just lives or dies! Instead, the population of organisms evolves. Recall that evolution is the change in allele frequencies, and only populations have allele frequencies. Individuals just have alleles.
  • Evolution is not a directed process with a fixed end point, or a best phenotype. Rather, the environment serves as a selective agent. No amount of planning on the part of the organism can predict whether an organism will be a good fit for the environment it finds itself in. An individual cannot try to evolve or anticipate the types of mutations it should have for future environmental change.
  • Organisms, and the genes they contain, do not behave for the good of the species. Rather, each individual lives and reproduces, which increases its representation in the gene pool, or it dies or fails to reproduce and is not represented in the gene pool. Those most represented after encountering a selective agent are considered the most fit for that environment, in that time and place.
  • Selection doesnt always result in the best possible fit of an organism to its environment because of constraints and trade-offs. Sometimes the same genes that code for a trait also cause a second, suboptimal trait to occur.
  • Evolution As An Emergent Property Of Life

    A key part of any definition of life is that living organisms reproduce. Lets now add a couple of observations:

    • The process of reproduction, while mostly accurate, is imperfect. When cells divide, they have to replicate their DNA. Although DNA replication is highly accurate, it still makes about 1 mistake in 10 million nucleotides. Over generations, the population will contain lots of heritable variation.
    • The population of a given type of organism will tend to grow exponentially, but will reach a limit, where the individuals have to compete with each other for the limiting resource

    Suppose some heritable variations make some individuals more competitive for the limiting resource what will happen?The individuals with superior variants will acquire more resources, and have more progeny. If the superior variants are heritable, then their progeny will have the same superior variants. Over generations, then, a larger and larger proportion of the population will consist of individuals with the superior heritable variants. This is biological evolution.

    Definition: Biological evolution is change in the heritable characteristics of a population over succeeding generations. In more technical terms, evolution is defined as change in the gene pool of a population, measurable as changes in allele frequencies in a population.

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    Phylogenetic Inference And Philosophy

    Section 1 served as an introduction to the history and problem of phylogeneticinference. In this section, we will look at how phylogenetics andphilosophy are intertwinedin particular, we will examine somefoundational debates in phylogenetics that have a distinctlyphilosophical flavor, and we will point out more traditionalphilosophical questions that the study of phylogenetics can shed lighton.

    At its core, phylogenetic inference is about evaluating competinghypotheses. In an important sense, phylogeneticists are faced withwhat philosophers of science would identify as a problem ofunderdetermination of theory by evidence.Multiple competing phylogenetic trees can explain the same data,though in conflicting ways it is the phylogeneticists task toidentify which of those hypotheses best explains those data. It willbe useful to separate the problem into two parts:

  • identifying what the evidence is and
  • constructing a phylogeny to explain the evidence we have.
  • In the case of phylogenetic inference, we are in the philosophicallyinteresting and puzzling situation where it seems that these twoquestions cannot really be separated.

    Primer And Introduction To Phylogenetics

    The Biological Classification of Paramecium â Name, History, and ...

    A phylogeny is a reconstruction of evolutionary history. Thus thediscovery of evolution is a good starting point for the history ofphylogenetics. While Darwin was not the first to propose that somespecies were genealogically related to others, it was On TheOrigin of Species that convinced many biologists toaccept common ancestry and to start building phylogenies. One of theimmediateand ongoingimpacts was the question this raisedin how phylogenies relate to taxonomies .

    Figure 1 Phylogenetic trees have become commonplace in biology research articles. This treedisplays a recent hypothesis on the relative placement of lungfish andcoelacanth in the evolutionary history of tetrapods .

    Pre-Darwinian taxonomy focused on classifying according to thenatural system where taxa were united into large groupsdue to their natural affinities . In aneffort to clarify the concept of affinity, Richard Owen used the termhomologue to refer to the same organ in differentanimals under every variety of form and function .Put into an evolutionary framework, the natural affinities unitingthese groups were regarded as the result of descent with modificationfrom common ancestors and homology has since become acentral term in comparative biology . To seehow homology relates to phylogenetic inference, as well as tointroduce some basic terminology, it will be useful to consider anexample phylogeny .

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    Terminology Of Phylogenetic Trees

    This is a bifurcating tree. The vertical lines, called branches, represent a lineage, and nodes are where they diverge, representing a speciation event from a common ancestor. The trunk at the base of the tree, is actually called the root. The root node represents the most recent common ancestor of all of the taxa represented on the tree. Time is also represented, proceeding from the oldest at the bottom to the most recent at the top. What this particular tree tells us is that taxon A and taxon B are more closely related to each other than either taxon is to taxon C. The reason is that taxon A and taxon B share a more recent common ancestor than they do with taxon C. A group of taxa that includes a common ancestor and all of its descendants is called a clade. A clade is also said to be monophyletic. A group that excludes one or more descendants is paraphyletic a group that excludes the common ancestor is said to be polyphyletic.

    The image below shows several monophyletic vs a polyphyletic or paraphyletic trees. Notice how the clades include the common ancestor and all of its descendants , while those labeled not a clade leave out some common ancestors or some descendants .

    From http://evolution.berkeley.edu/evolibrary/article/side_0_0/evo_06

    The video below focuses on terminology and explores some misconceptions about reading trees:

    Structure Of Phylogenetic Trees

    A phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domainsBacteria, Archaea, and Eukaryadiverge from a single point and branch off. The small branch that plants and animals occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees dont show a common ancestor but do show relationships among species.

    Figure 2. Both of these phylogenetic trees shows the relationship of the three domains of lifeBacteria, Archaea, and Eukaryabut the rooted tree attempts to identify when various species diverged from a common ancestor while the unrooted tree does not.

    Figure 3. The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy.

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    Misconceptions And How To Correctly Read A Phylogenetic Tree

    Trees can be confusing to read. A common mistake is to read the tips of the trees and think their order has meaning. In the tree above, the closest relative to taxon C is not taxon B. Both A and B are equally distant from, or related to, taxon C. In fact, switching the labels of taxa A and B would result in a topologically equivalent tree. It is the order of branching along the time axis that matters. The illustration below shows that one can rotate branches and not affect the structure of the tree, much like a hanging mobile:

    http://evolution.berkeley.edu/evolibrary/article/%3C?%20echo%20$baseURL %20?%3E_0_0/evotrees_primer_08

    Hanging bird mobile by Charlie Harper

    It can also be difficult to recognize how the trees model evolutionary relationships. One thing to remember is that any tree represents a minuscule subset of the tree of life.

    The time axis also allows us to measure evolutionary distances quantitatively. The distance between A and Q is 4 million years . The distance between A and D is 6 million years, since they split from their common ancestor 3 million years ago.

    Phylogenetic trees can have different forms they may be oriented sideways, inverted , or the branches may be curved, or the tree may be radial . Regardless of how the tree is drawn, the branching patterns all convey the same information: evolutionary ancestry and patterns of divergence.

    Using Mega5 On Macintosh Computers

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    The Save and Open dialogs are Windows-like and may be unfamiliar to Mac users. A document detailing navigation in MEGA 5 for Mac can be downloaded from .

    Some Macintosh users have reported problems running MEGA5 for Mac on their machines they need not, however, do without MEGA5. There are several virtual machine programs such as Parallels and VMFusion that will allow a Macintosh to run the Windows operating system. They both necessitate buying a copy of Windows and installing it in the virtual machine, but once that is done and MEGA5 for Windows is installed on that virtual machine, MEGA5 is as convenient and easy to run as it would be on a dedicated Windows computer. In addition, the user then has access to the entire world of Windows programs, some of which are actually as good as Macintosh programs.

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