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Linnaeus and the Science of Systematics: Taxonomy, Phylogeny, and the Great Tree of Life -, Exams of Theory of Evolution

An overview of systematics, the scientific study of biological diversity and evolutionary history of organisms. It covers topics such as taxonomy, phylogeny, nomenclature, and the work of carolus linnaeus. The importance of inferring phylogenetic history through similarities and common ancestry, as well as the challenges and methods used in this field.

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Pre 2010

Uploaded on 08/18/2009

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Chapter 2 THE TREE OF LIFE:
CLASSIFICATION AND PHYLOGENY
We have grouped organisms for easier study by comparing similarities and differences.
SYSTEMATICS: the study of the diversity of organisms and their comparative and evolutionary
relationships. It includes comparative anatomy, comparative biochemistry, comparative
physiology, etc.
CLASSIFICATION OR TAXONOMY is the ordering of organisms into groups. It includes the
principles procedures used in classification.
PHYLOGENY: refers to the evolutionary history of a species or group of species in terms of
their derivations through evolutionary processes; which species share a common ancestor, which
species share a more distant ancestor, etc.
Systematics is the study of biological diversity and evolutionary history of organisms.
Systematics includes...
Taxonomy, the science of identifying and classifying organisms.
Phylogenetics, the study of the evolutionary history of organisms.
Nomenclature, the system used in naming organisms.
CLASSIFICATION
The present system of nomenclature was devised by Carolus Linnaeus (Carl von Linne), a
Swedish botanist who live in the 18th. Century.
Linnaeus published in 1753 a book called Species Plantarum, "the kinds of plants".
Binomial system of nomenclature: Genus + species epithet = scientific name of the plant.
Hierarchical classification: groups within groups.
A taxonomic grouping 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, e.g. superfamily or subspecies.
Since Darwin, most systems of classification attempt to reflect phylogenetic relationships.
It is difficult to find an unbroken line of ancestors that connect the different groups in questions.
Natural processes often destroy fossil evidence.
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Chapter 2 THE TREE OF LIFE:

CLASSIFICATION AND PHYLOGENY

We have grouped organisms for easier study by comparing similarities and differences. SYSTEMATICS : the study of the diversity of organisms and their comparative and evolutionary relationships. It includes comparative anatomy, comparative biochemistry, comparative physiology, etc. CLASSIFICATION OR TAXONOMY is the ordering of organisms into groups. It includes the principles procedures used in classification. PHYLOGENY : refers to the evolutionary history of a species or group of species in terms of their derivations through evolutionary processes; which species share a common ancestor, which species share a more distant ancestor, etc. Systematics is the study of biological diversity and evolutionary history of organisms. Systematics includes...  Taxonomy , the science of identifying and classifying organisms.  Phylogenetics , the study of the evolutionary history of organisms.  Nomenclature, the system used in naming organisms.

CLASSIFICATION

The present system of nomenclature was devised by Carolus Linnaeus (Carl von Linne), a Swedish botanist who live in the 18th. Century. Linnaeus published in 1753 a book called Species Plantarum, "the kinds of plants".  Binomial system of nomenclature: Genus + species epithet = scientific name of the plant.  Hierarchical classification: groups within groups.  A taxonomic grouping 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, e.g. superfamily or subspecies. Since Darwin, most systems of classification attempt to reflect phylogenetic relationships. It is difficult to find an unbroken line of ancestors that connect the different groups in questions.  Natural processes often destroy fossil evidence.

Taxonomists have to weigh the evidence provided by similarities between organisms. Darwin proposed that on occasion, a species may split into two species, which at first are very similar to each other but with time diverge, become more different. Each of these two species may in turn split into two other daughter species, and so on. Closely related species are descended from a relatively recent common ancestor; distantly related species are descended from a more remote ancestor, farther back in time. In Darwin’s words, all species extant and extinct, form the Great Tree of Life, a phylogenetic tree. Darwin’s hypothesis proposes that a hierarchical classification should reflect a historical process that produced organisms with true genealogical relationship: phylogeny.  Classification should reflect the real history of evolution.

INFERRING PHYLOGENETIC HISTORY

Similarity and common ancestry A feature or a trait is called a character.  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 character states , e.g. white or purple flowers, hairs long or short, A base or C base in particular nucleotide sequence.  Ancestral or plesiomorphic characters are found in the common ancestor of daughter species.  Derived or apomorphic characters have evolved from the ancestral character. o Synapomorphic characters are derived characters found in two or more species and suggest a close common ancestor. Shared derived characters are evidence of evolutionary relationship. Phylogenetic classification should be monophyletic. Monophyletic means that all the members of a taxon regardless of rank, are descendants of a common ancestor. Organisms in a polyphyletic group evolved from different ancestors.

Evaluating phylogenetic hypotheses The phylogenetic tree obtained from a set of data is a hypothesis that is provisionally accepted. Additional data may lead to modify or abandon the hypothesis. The best way to of confirming a phylogenetic hypothesis is to see if it agrees with independent data, e.g. morphological characters and DNA sequences. Computer models and experimental populations of bacteria have been used to test the validity of phylogenetic methods by applying them to phylogenies that are absolutely known.

MOLECULAR CLOCKS

Evolutionary or molecular clock : Some workers assume that mutations are incorporated into the genome at 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 hemoglobin chain differs from that of other vertebrates (human, chicken, carp, salamander) by similar numbers of AA changes. DNA sequences may evolve and diverge at a 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 molecular evolutionary clock exists, it can provide a simple way of estimating phylogeny. Information from the fossil record on the absolute time of divergence of certain taxa can be used to calibrate the molecular clock, e.g. the oldest cercopithecoid monkey fossil is dated at 25 My, providing the minimal estimate time since divergence between the rhesus monkey and the hominoids. See example on page 33. The formula D = 2rt can be used to estimate the divergence time between two species that have not left a good fossil record.  D = proportion of base pairs that differ between the two sequences.  r = the rate of divergence per base pair per My  t = the time in My since the species’ common ancestor.  2 represents the two diverging lineages. The rate of sequence divergence is not necessarily constant.  The rates are quite similar between taxa that are closely related.  Distantly related taxa often have rather different evolutionary rates.

GENE TREES

A phylogeny of genes is called a gene tree 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 other members of the population in which there had been no mutation. In preparing the gene, the sequences that differ the least from each other have the closest ancestor-hemoglobin chain differs from that of other descendant relationship; the most closely related haplotypes are connected to each other by the smallest possible number of mutations. See example on pages 34 and 35. DIFFICULTIES IN PHYLOGENETIC ANALYSIS

  1. 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 number of independent characters is difficult to decide. This difficulty also exists at the molecular level, e.g. rRNA molecule includes short sequences whose bases must pair to for stems so changes in those sequences are not independent.
  2. Homoplasy is very common.  It is unwise to rely on particular phylogenetic estimate if other phylogenetic hypotheses imply just a few extra evolutionary changes.
  3. The process of evolution often erases the traces of prior evolutionary history.  If the taxa under study diverged long ago or evolved very rapidly, many of their characteristics will have diverged so greatly that homologous characters may be difficult to discern.  In DNA multiple substitutions may occur at a site over the course of time erasing previous synapomorphies.  If the same substitution occurs in parallel lineages, convergent evolution will occur
  4. Some lineages diverge so rapidly that there is little opportunity for the ancestors of each monophyletic group to evolve distinctive synapomorphies.  A burst of diversification called adaptive radiation or evolutionary radiation produces different adaptations in the lineage.
  5. An accurately estimated gene tree may imply the wrong species phylogeny.