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Phylogeny and Genomes

In this post you we will learn how biologist use genomes to get information for phylogeny, how to choose the right genomes for comparison and the mechanism behind the differences and evolution of genomes over the years. So braise yourself of a blast of Molecular Science in your face. Hopefully after reading this post you will be enlightened on the topic of Genomes. Have fun What Are Genomes? Genomes are places where DNA sequences that code instructions for specific living functions that are passed through from parent to offspring are found. The process of evolution is when these DNA sequences undergo alterations through the process of mutation and recombination. What makes this information so valuable for phylogeny you must be asking. This molecular data help in comparing relationships between two distant group of organisms that do no t share common morphological attributes. This also allows reconstruction of anomalous or unresolved phylogenetic trees. We cans say this because when we compare the genes of distant groups of organisms we can see common genes called conserved genes. They are conserved because these are DNA sequences that are responsible for coding critical functions in the development of an organism. Important Terms: genomes, mutation, recombination How Do We Know What To Use? Typically we use non-coding regions of the DNA are best used since this is where mutations typically occur another on is to use amino acid sequences of proteins because they play crucial part in the development of an organism. But there are also other reason why we use these data. It also depends on what relationship you are trying to determine. The rule of thumb that I like to remember is that the father the less change and the closer the rapider change. This simply means that if you are looking to deuce relationships among groups of organism that have diverged million years ago, you use a DNA sequence that mutates relatively slow. Examples being DNA that codes for ribosomal RNA. Then on the other hand when you want to compare the relationship of closely related organism, you use DNA sequence that mutates relatively fast to show evolutionary events. Example of these kind of DNA sequence is that of mitochondrial DNA which mutates rapidly. Important Terms: non-coding regions, ribosomal RNA, mitochondrial DNA Why Does Mutation Happen? The reason why this happens is because of the mechanism of gene duplication. Gene duplication is a genetic event wherein one copy of a DNA code is being duplicated and reinserted to an organism’s DNA. This happens naturally during the process of DNA replications. During duplication, mutations occur in the gene which could result to formation of new proteins with new functions. Due to repeated process of gene duplications this lead to the creation of gene families. These are groups of similar genes within an organisms’ genome. Homologous genes or homologs is what we refer to similar genes. Homologs have two types. On being orthologous homologs and the other being paralogous homologs. Orthologous genes, comes form the Greek word “orthos” which means exact. This means that orthologous genes refer to the exact similar genes that preforms similar function but are found in different organism. An example being the gene for cytochrome c of humans and dogs. On the other hand paralogous genes, comes from the Greek word “para” which means parallel.  This means that due to gene duplication the gene is copied in that same organism but may have different functions. An example of this is the olfactory receptor gene among humans. Fun Fact: Humans and mice share 99% of orthologous genes Important Terms: gene duplication, homologous genes, orthologous homologs, paralogous homologs

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Morphological Vs. Molecular

In this post you will learn what types of data biologist use to construct accurate phylogenetic tree. We will discuss what is morphological and molecular data, how are they different from one another, how they are used to construct phylogenetic trees and what we can infer from said phylogenetic trees. Hope at the end of reading this post you will have a better understanding on this topic. Have fun :)

Morphological and Molecular Data

In constructing and reconstructing phylogenies, biologist use two important characteristics. These being morphological and molecular data. Right now you must be wonder what is morphological and molecular data. Well I got the answer for you. Morphological data comes from morphology and as we know from my pervious post (hope you read that ;) ) we learned that “morphe” is the Greek word for form. So morphological data describes the features of internal and external forms or appearances of living organism and fossils. It is very useful for detecting and explaining variation patterns, determine evolutionary relationships and identifying the species of an organism. On the other hand molecular data includes use of DNA sequence for genes and amino acids sequences for proteins to determine evolutionary relationships and identify the species of an organism. Examples of friquently used data are rRNA (ribosomal), cytochrome c ocidase I, cytochrome-b genes, rbcL genes and matK genes. When comparing molecular data if two sequences differ ar only one or a few sites, then most likely they are homologous, and very closely related. Otherwise, the sequence is a coincidental matches or molecular homoplasy. Important Terms: morphological, molecular

Inferring Phylogenetic Trees

Since we used morphological and molecular data to construct these phylogenetic trees we can say that we have tangible evidence on the relationships between each taxa and their common ancestors. We know that phylogenetic trees have branches with proportional length to the amount fo evolutionarily change. The longer the branch, the more evolutionary (genetic) change has occurred. Then to makes sure whether they are accurate we have a principle called maximum parsimony. Maximum parsimony basically states that the simples tree is most likely the true one. In morphological trees, the most parsimonious tree has the fewest evolutionary changes . In molecular trees, the most parsimonious tree has the fewest base change. Important Terms: maximum parsimony

Phylogenetic Trees as Hypothesis

At the end of the day nothing is really set in stone. All phylogenetic trees represent hypothetical relationships of organism in the tree supported by both morphological and molecular data. Thinking of phylogenetic tress as hypothesis allows us to make and test predictions on the assumptions that our hypothesis is correct. We call this as phylogenetic bracketing, it is when we infer wherein the likelihood of unknow traits of organisms is based on their position in the phylogenic tree. This works by comparing an extinct organism to its nearest extant relatives. Us thinking at phylogenetic trees are hypothesis makes them easy to change or to improve based on new evidences and it also helps us understand the taxa of the past by finding the patterns seen in the present

Important Terms: hypothesis, phylogenetic tree, phylogenetic bracketing

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Phylogenetics?

This post aims to teach you on what phylogenetics is, how phylogenetics is represented, and what a phylogenetic tree is and characteristics used in phylogenetic trees.  I really hope that after reading this you will have a better understanding of phylogenetic. :)

What is phylogenetics?

To understand why phylogenetics is you must first understand why phylogeny is. Phylogeny refers to the evolutionary history and relationships of species. It describes the morphological and molecular change that occurred in the species’ lineage from its origin to most recent ancestor. With that said phylogenetics is the dynamic discipline that is applied to systematics and aims to uncover evolutionary processes behind the origin of species

Important terms: Phylogenetics, Phylogeny, morphological, molecular

What are phylogenetic trees?

Phylogenetic trees serve as the visual representation of phylogeny of taxa. In phylogenetics there are two types of trees used to understand the evolutionary relationships between taxa. First is the cladogram, they represents the hypothetical relationship between taxa and heir recent common ancestors. Now the second is called a phylogram, just like a cladogram it also represents  the evolutionary relationships of taxa and their recent common ancestors but in addition to that have the branch lengths proportional to evolutionary time. To further understand phylogenetic trees you must be familiar with its parts:

                         Figure 1:  Components of a phylogenetic tree

root - represent the recent common ancestors of all the organisms

branches/edges - represent lineages for the taxa of interests

branch point/nodes - speciation events from a common ancestor where  one lineage splits into two or the common ancestor itself

Leaves - tips of the branches, can be ingroup (species of interest) or    outgroup (distant relative of ingroup)

Important terms: Phylogenetic tree, cladogram , phylogram, root, branches,      nodes, ingroup, outgroup

What characteristics are used in phylogenetic trees?

Characteristics which are being used phylogenetics trees are very important because they are usually what separates the taxa from one another. For a general thought character states can be analogous (character states with similar functions found in distantly-related organism) or homologous (chanter states have similar structures due to common ancestry). An example for analogous characters is the wings of bird and insects, both serve the same function of flight but evolved separately from one another. Then an example of homologous characters is limb pattern (humerus, radius, ulna, carpals, and metacarpals) of the wings of bats, flippers of dolphins and forelimbs of anteaters, moles, horses, and monkeys. For phylogenetic trees we have 2 types of characteristics that relate to relatedness. This being: plesiomophy and apomorphy. Plesiomophy comes the Greek words “plisiazo” which means near/ancestral and “morfi” which means from. From that  plesiomorphy is the ancestral or primitive feature. Then apomorphy comes from the Greek word “apo” which means derived. So by that apomorphy is the  derived characteristics.

Important terms: Analogous, homologous, plesiomorphy, apomorphy

References: 

Figure 1. Components of a phylogenetic tree. Adapted from “Taxonomy and  Phylogeny: Figure 2” by R. Bear et al., 2016. Retrieved from https://cnx.org/contents/24nI-KJ8@24.18:EmlvXoDL@7/Taxonomy- and-phylogeny. CC BY 4.0

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hello world.

Hey there dear reader. Welcome to the BiologistEpicenter! I am your writer Aljo Mark Erap or you can just call me by my username (paleinfluencercat). This blog will serve as a general space where you can share things related to Biology.  From interesting facts of animals to the inner mechanisms of molecular biolology anything is welcome here. Just message me and ill try to post it (maybe). Anyways done reading the introduction lets get to the learning.