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37 Cards in this Set

  • Front
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What is classification or taxonomy?

it is the ordering of organisms into groups, it includes the principles procedures used in classification



What is phylogeny?

is the evolutionary history of species in terms of their derivations through evolutionary process, for example which species share a common ancestor, or which species share a more distance ancestor

What is systematics?

classifications of organisms using phylogenetic relationships. It includes comparative anatomy, comparative biochemistry, and comparative physiology which as a result shows biological diversity and evolutionary history of organisms



Systematics include...

taxonomy- the science of studying and identifying organisms


Phylogenetics-the study of the evolutionary history of organisms


nomenclature- the system used in naming organisms



The present system of nomenclature was devised by?

Carolus Linnaeus, a swedish botanist who lived in teh 18th century. Linnaeus published a book in 1753 called Species Plantarum, "the kinds of plants"

It included a:


Binomial system of nomenclatures: Genus + species = scientific name of the plants




Hierarchical classification: groups within groups




The levels of classification are referred as taxonomic categories, phylum, class




A particular group of organisms is called a taxon




Taxonomy is hierarchical: taxa are grouped into broader taxa

Species are grouped into genera(sing. genus)




Genera into families; families into orders, orders into classes; classes into divisions; divisions into kingdoms.




There are intermediate taxonomic categories, Ex. superfamily of subspecies




Higher taxa are those above the species level



Since Darwin, most systems ofclassification attempt to reflect phylogenetic relationships. It is difficult to find an unbrokenline of ancestors that connect the different groups in questions. Natural processes often destroy fossil evidence.Taxonomists have to weigh the evidenceprovided by similarities between organisms.

Darwin wrote On the Origin ofSpecies in 1859.Darwin proposed that on occasion, aspecies may split into two species, which at first are very similarto each other but with time diverge, become more different. Each of these two species may in turnsplit into two other daughter species, and so on. Closely related species are descendedfrom a relatively recent common ancestor (monophyletic);distantly related species are descended from a more remote ancestor,farther back in time. In Darwin’s words, all species extantand extinct form the Great Tree of Life, a phylogenetic tree.



A phylogenetic tree shows monophyleticgroups and their common ancestor. Phylogenetic trees are proposed basedon the characteristics shared by the taxa. They represent evolutionaryrelationships.Darwin’s hypothesis proposes that ahierarchical classification should reflect a historical process thatproduced organisms with true genealogical relationship: phylogeny. Classification should reflect the real history of evolution.



INFERRING PHYLOGENETIC HISTORYSimilarity and common ancestry

A feature or a trait is called acharacter. A character may be a morphological characteristic, e.g. presence of hairs, shape of shell, etc. A character may also be a trait at the cellular, biochemical or molecular level, e.g. a particular nucleotide sequence.A character may have several characterstates, e.g. white or purple flowers, hairs long or short, “A”base or “C” base in a particular nucleotide sequence.

Ancestral or plesiomorphic characters are found in the common ancestor of daughter species.

Ancestral or plesiomorphic characters are found in the common ancestor of daughter species.

Derived or apomorphic charactershave evolved from the ancestral character.

Derived or apomorphic charactershave evolved from the ancestral character.

Synapomorphic characters are derived characters found in two or more species and suggest a close common ancestor.

Synapomorphic characters are derived characters found in two or more species and suggest a close common ancestor.

Shared derived characters are evidenceof evolutionary relationship.

Shared derived characters are evidence of evolutionary relationship.

Phylogenetic classification should be monophyletic.

Monophyletic means that all the membersof a taxon regardless of rank are descendants of a common ancestor.

The more recent two species share acommon ancestor, the more closely related these two species are.

The more recent two species share acommon ancestor, the more closely related these two species are.

A monophyletic group is also called aclade.

A monophyletic group is also called aclade.

Organisms in a polyphyletic groupevolved from different ancestors.

Organisms in a polyphyletic groupevolved from different ancestors.

Complications in inferring phylogeny

Degree of relationship is based on howrecent they share a common ancestor and not on similarities.Taxa may be similar because they shareancestral character states or derived character states, but only thederived character states that are shared among taxa indicatemonophyletic groups and enables us to infer phylogeny successfully. Character states that are restricted toa single lineage are sometimes called autapomorphies.

Character states that are restricted toa single lineage are sometimes called autapomorphies.

Homology: same feature in different species is derived from a common ancestor, e.g. the forelimb of vertebrates.



Homoplasy: a feature that has evolved two or more times independently of the other and thus do not have a common origin.

Parallelism: parallelism results in homoplasy; it is an evolutionary process; a similar feature occurs in different species but their immediate common ancestor was different and did not have the feature. The similar feature occurs in different but related species, but it is not present in their immediate common ancestor. They are likely to have similar evolutionary mechanisms. They are functional adaptations. E.g. Anteater features in eutheria, metatheria and prototheria.

Convergence: convergence results in homoplasy; is an evolutionary process; two species with similar phenotype whose common ancestor is very far in the distant past. Independent genetic origin. The evolutionary mechanisms are different. E.g. the hydrodynamic morphology of marine predators from the widely separated fish, reptile and mammalian classes

Some scientists do not consider thedistinction between parallelism and convergence meaningful.Look at the following paragraph thatexplains the position of eliminating the distinction between paralleland convergent evolution. This complete article can be found at:http://people.ibest.uidaho.edu/~bree/courses/19_Arendt_2007.pdf

"Biologistsoften distinguish 'convergent' from 'parallel' evolution. Thisdistinction usually assumes that when a given phenotype evolves, theunderlying genetic mechanisms are different in distantly relatedspecies (convergent) but similar in closely related species(parallel). However, several examples show that the same phenotypemight evolve among populations within a species by changes indifferent genes. Conversely, similar phenotypes might evolve indistantly related species by changes in the same gene. We thus arguethat the distinction between 'convergent' and 'parallel' evolution isa false dichotomy, at best representing ends of a continuum. We cansimplify our vocabulary; all instances of the independent evolutionof a given phenotype can be described with a single term -convergent.""If the use ofthe terms 'parallelism' and 'convergence' cannot be associated with aclear dichotomy, either at a phylogenetic level or a molecular level,then their continued use is not justified and can even be misleading.They are relics of a time when we could not evaluate the underlyingcauses of phenotypic similarity and were confined to inferences basedon comparative anatomy. These terms are also relics of a time whenthere was not an appreciation of the complexity of genetic anddevelopmental networks that underlie the determination of simplephenotypic traits, such as coloration. We argue that this might be agood time to simplify our vocabulary. We need only one term todescribe the independent evolution of phenotypic similarity.'Convergent evolution' will do nicely."JeffArendt and David Reznick, Convergenceand parallelism reconsidered: what have we learned about the geneticsof adaptation?http://people.ibest.uidaho.edu/~bree/courses/19_Arendt_2007.pdf

Parallelism and convergence (homoplasy)can lead to false conclusions about homology.

Evolutionary reversal of acharacter can also occur.

Evolutionary reversal is the change of an apomorphic character to one similar to an ancestral character, e.g. dolphins look like fish now, an ancestral character, but they were terrestrial at one time with the appearance of a terrestrial mammal.

Taxa may be similar because…




They share ancestral character states.


They share derived character states.


They possess homoplasious characters states.



Taxa may be similar because…



They share ancestral character states.


They share derived character states.


They possess homoplasious characters states.

The method of maximum parsimony

Parsimony refers to theprinciple that states that the simplest explanation requiring theleast number of undocumented assumptions, should be preferred overmore complicated hypotheses that require more assumptions for whichevidence is lacking.




The best estimate of true phylogeny requires the fewest number of evolutionary changes.



The ingroup refers to themonophyletic group of species whose phylogeny we want to infer.

The outgroup is made of moredistantly related taxa.

Sister groups are groups ofspecies derived from a common ancestor that is not shared with anyother group.

Sister groups are groups ofspecies derived from a common ancestor that is not shared with anyother group.

Evaluating phylogenetic hypotheses

The phylogenetic tree obtained from aset of data is a hypothesis that is provisionally accepted.Additional data may lead to modify orabandon the hypothesis.The best way to of confirming aphylogenetic hypothesis is to see if it agrees with independent data,e.g. morphological characters and DNA sequences. See the example on page 32, Fig. 2.11.Computer models and experimentalpopulations of bacteria have been used to test the validity ofphylogenetic methods by applying them to phylogenies that areabsolutely known.

MOLECULAR CLOCKS

Evolutionary or molecular clock:Some workers assume that mutations are incorporated into the genomeat a fairly regular rate. There is evidence to this effect.




E.g. the shark sequence of the α-hemoglobin chain differs from that of other vertebrates (human, chicken, carp, salamander) by similar numbers of AA changes.

DNA sequences may evolve and diverge ata constant rate.

Evolutionary differences between organisms arise from mutational differences.




The greater the number of mutational differences, the greater the evolutionary distance between organisms.





To the extent that the molecularevolutionary clock exists, it can provide a simple way of estimatingphylogeny.

information from the fossil record onthe absolute time of divergence of certain taxa can be used tocalibrate the molecular clock, e.g. the oldest cercopithecoid monkeyfossil is dated at 25 My, providing the minimal estimate time sincedivergence between the rhesus monkey and the hominoids. Seeexample on pages 33-34.

Example on page 34:

Theformula D = 2rtcan be used to estimate the divergence time between two species thathave not left a good fossil record.




D = proportion of base pairs that differ between the two sequences, e.g. 0.0256.




r = the rate of divergence per base pair per My, e.g. 0.001534




t = the time in million years since the species’ common ancestor.




2 represents the two diverging lineages.




t = D/2r or 8.3 My is the best estimate of when the two species diverged from their common ancestor.

The rate of sequence divergence is notnecessarily constant.

The rates are quite similar between taxa that are closely related.




Distantly related taxa often have rather different evolutionary rates.




The rate can be used to estimate the absolute age of evolutionary events, such as the origin of taxa.



GENE TREES

Genes replicate, different copies of agene, within a single species or more than one species, have ahistory of descent from a common ancestral gene just as species do.




The historical relationship amongvariant DNA sequences of a gene (haplotype) can be used toconstruct the phylogeny of a gene, a gene tree.




Haplotype refers to a group of genes that are found in an adjacent place in a chromosome and are inherited together.





A phylogeny of genes is called a genetree or gene genealogy.

A DNA sequence is called a haplotype.

When a mutation occurs in an individual, the ancestral haplotype continues to exist in the othermembers of the population in which there had been no mutation.

In preparing the gene tree, thesequences that differ the least from each other have the closestancestor-descendant relationship; the most closely related haplotypesare connected to each other by the smallest possible number ofmutations.


See example on page 36

DIFFICULTIES IN PHYLOGENETIC ANALYSIS




Evaluating characters is difficult


- Deciding whether or not organisms have the same character state often requires extensive knowledge of anatomical details and is not an easy or trivial task




- The # of independent characters is difficult to decide. This difficulty also exists at the molecular level, e.g. rRNA molecules includes short sequences whose bases must pair to form "stems" so changes in those sequences are not independent; some mammals have two incisors, a canine, three premolars, and four molars on each side of the haw, while others do not have teeth, does this represent the loss of one character or four characters?