Chapter 26 - Biology - Phylogeny And Tree Of Life

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Chapter 26 Biology Phylogeny And Tree Of Life

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This is the discipline focused on classifying organisms by evolutionary relationships
This is the term for how organisms are named and classified
Binomial nomenclature
This is the two-part format of scientific name instituted by 18th century Linnaeus. The first part is the genus to which the species belongs, and the second is a specific epithet for that species
Homo sapien in latin
wise man
Hierarchal Classification
This method, founded by Linnaeus, groups species into hierarchy of increasingly inclusive categories. Species that appeared closely related were grouped into the same genus. Higher level classification are usually assigned by morphology.
Order of hierarchal classification 
From smallest to largest: species, genus, family, order, class, phyla, kingdom, domain
term for the unit at any level of hierarchy
Systematists propose classification be based entirely on evolutionary code and relationships, using this.
Advantage of Phylogenetic tree
This is because this represents a hypothesis about evolutionary relationships.
Branch points
These represent relationships depicted as series of dichotomies. Each of these represents divergence of two lineages from common ancestor
Sister taxa
these are groups that share immediate common ancestors; closest relatives to one another
rooted tree
this is a branch point within a phylogenetic tree that represents the last common ancestor of all taxa on the tree
this is a branch point from which more than 2 descendants emerged
Limitations of Phylogynetic trees
These include its inability to indicate the real ages of a species; not time sensitive unless otherwise indicated. 
Advantages of Phylogenetic trees
These include information we can learn. For example, when mapping this for maize, or corn, biologists can track relatives thru ancestry and find genes that may allow for genetic engineering. Also, bioterrorism attempts can be thwarted because these helped trace the source and strain of mailed anthrax.
What systemologists use to infer phylogeny
Morphology, genes, and biochemistry of relevant organisms.
Dna and genes are homologous if...
...they are descended from sequences carried by common ancestors
Just because two species have a great morphological divergence doesn't mean...
...they have a large genetic divergence. example: the hawaiin silversword looks different on each island, but still comes from same ancestor.
this is the term for similarity due to convergent evolution rather than shared ancestry
convergent evolution
this occurs when similar environmental pressure and natural selection produce similar, or analogous, adaptations in organisms from different evolutionary lineages. (Example: australian moles are marsupials, while north american moles are eutherians. both look very similar even tho the share a very old ancestor who wasn't even mole-like.)
How bats and birds illustrate the importance of distinguishing homology from analogy. 
Because both fly, one may assume the both come from the same ancestor. But really bone structure in the wing of a bat is more similar to cats than birds.
analogous structures that arose independently
How to find homoplasies
complexity: the more points of resemblance 2 complex structures have, the more likely they are homologous. example: human and chimp skull bones are similar, almost bone for bone identical, it is unlikely we come from different origins. this is because the genes for bone growth were passed down from a common ancestor. 
the 4 bases made up of nucleotides in DNA
A (adenine) G (guanine) C (cytosine) and T (thymine)
Steps for finding molecular homologies
first, sequence molecule's DNA, then align comparable sequences of 2 different species. If related, sequences probably differ at very few sites. Insertions and deletions in DNA sequence accumulate over time.
Molecular systematics
This is the discipline that uses DNA and other molecular data to determine evolutionary relationships
This is an approach to inferring phylogeny based only on common ancestry.
these are the groups biologists place species into. The include ancestral species and all its descendants.
Monophyletic (clade)
This signifies a clade is like a taxon because it consists of an ancestor and all its descendants.
paraphyletic (clade)
this clade consists of an ancestor but on some descendants.
polyphyletic (clade)
This clade includes descendants with different ancestors 
Shared ancestral character
This is a character that originated in the ancestor of a taxon. example: backbone
shared derived character
this is an evolutionary novelty unique to a particular clade or generation. example: hair on mammals
this is a species or group of species from an evolutionary lineage known to have diverged before ingroup. polytomy can be found in where ingroup diverged from outgroup.
this is the group being studied and lineage thereof.
Maximum parsimony
this is used in creating phylogenetic trees. The principle is based on Occam's Razor, to investigate the simplest explanation that is consistent with facts. example: for phylogenies based on DNA the most parsimonious tree requires the fewest base changes. 
Maximum likelihood
given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events.
phylogenetic bracketing
this is a prediction (via parsimony) that features shared by 2 groups are present in an ancestor (example: birds came from theropods, a bipedal ancestor of crocs as well. as a result, crocs can also sing to attract mates and defend their territories, have 4 chambered hearts, and build nests and brood young. Biologists assume there was one dino ancestor for these two species who shared these traits.
Advatanges of Molecular systematics
Firstly, these help us understand phylogenetic relationships that cannot be found nonmolecularly, like comparative anatomy. It helps in finding relationships between, for example, animals and fungi, and where there is no fossil record. 
gene families
groups or related genes within an organism's genome
orthologous genes 
these are homologous genes that are found in different species because of speciation. example: humans and dogs share these.
paralogous genes
these result from gene duplication; they are found in more than one copy in same genome. example: different odors recognized by nose are thanks to these.
Molecular clocks
these help track evolutionary time; they are a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes evolve at constant rates. the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since species branched from common ancestor.
Problems with molecular clocks
These include the problem that these things can only show, in most cases, certain trends because of erratic genome behavior; some genes evolves at difference rates in different groups of organisms
Neutral Theory
this theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by darwinian selection. This was developed in the 1960's by Jack King and Thomas Jukes (UC Berkeley) and Motoo Kimura (Japan)
First two kingdoms arranged by scientists
Plants and Animals, with bacteria in plants because it had a rigid cell wall. unicellular eukaryotes and chloroplasts also considered plants, along with fungi. Those like Euglena, who could move but were photosynthetic were in both kingdoms.
Animal requirements to be placed in first ever kindgom
unicellular organisms that move and digest food. 
5 Kingdoms
Monera (prokaryotes), protista (diversa; mostly unicellular organisms), plantae, fungi, animalia. Developed in 1960's as a revision of older version.
Fundamental problem with  5 kingdoms
some prokaryotes differed from each other as much as they did from eukaryotes
3 domains
bacteria, archea, and eukarya 
Bacteria Domain
This contains most of the known prokaryotes
Archea Domain
This contains a diverse group of prokaryotes that inhabit a variety or environments 
This contains organisms that have cells that contain true nuclei; single celled organisms, multi celled organisms like plants and fungi, and animals
Single celled organisms
this type composes the majority of life on earth historically
Monera and Protista
both of these kingdoms are obsolete because both are polyphyletic.
First major Split in the history of life
This event is when bacteria diverged from other organisms
rRNA genes
these have evolved so slowly that homologies between distantly related organisms can still be detected today. The tree of life is based largely on sequence comparisons of these.
Horizontal gene transfer
This is the process in which genes are transferred from one genome to another thru mechanisms such as exchange of transposable elements, viral infections, and even fusion of organisms. For example: the first eukaryote may have arisen thru a fusion between an ancestral bacterium and an ancestral archaea. 
Ring of life
This hypothesis is an alternative to traditional thinking about the tree of life. Horizontal gene transfers were common in early Earth, as eukaryotes may have arisen from endosymbiosis between bacteria and archaea