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

Download Linnaeus and the Science of Systematics: Taxonomy, Phylogeny, and the Great Tree of Life - and more Exams Theory of Evolution in PDF only on Docsity! 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. 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.  Some species are polymorphic for the same haplotypes, probably inherited from a polymorphic common ancestor. These haplotypes do not accurately indicate the phylogeny of these species. HYBRIDIZATION AND HORIZONTAL GENE TRANSFER Many species of plants and a few species of animals have arisen from hybridization. Hybridization is the interbreeding of two ancestral species. The hybrid species phylogeny based on different genes will differ; it will be incongruent. Evolution by hybridizations is called reticulate evolution. See fig. 2.20, p. 39. Horizontal or lateral gene transfer usually incorporates just a few genes of one species into the genome of another species. This is in contrast of the vertical gene transfer that occurs between parents and offspring. Lateral gene transfer may occur via a virus, e.g. a group of genes transferred from monkeys to cats by a viral vector. Lateral gene transfer is very important in the evolution of bacteria. In bacteria genes may be transferred laterally by  A phage.  Uptake of naked DNA released from dead cells  Conjugation Phylogenic incongruence and several other lines of evidence have shown that lateral transfer has provided various bacteria with genes for antibiotic resistance, for the ability to invade hosts and cause disease, and for adaptations to extreme environments such as hot springs.