1 molecular evolution molecular phylogenetics evolution of - - PDF document

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Introduction to Molecular Evolution (BIOL 3046) Course website: www.biol3046.info What is molecular evolution? = process + outcome

Population genetics Molecular biology Genetic diversity

Genes Proteins Genomes

Organism diversity:

Populations Species Above

Felis Canis Ursus Bos Hippopotamus Physeter Balaenoptera Rhinoceros Equus

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molecular evolution molecular phylogenetics evolution of molecules bioinformatics genomics population genetics molecular ecology

MOLECUALR PHYLOGENETICS: The principles and practice of inferring evolutionary relationships from molecular data. GENOMICS: The study of the structure and functional properties of genomes and the function of genes within a genomic context. BIOINFORMATICS: The science of applying computer technology and statistical techniques to the management and study of biological information.

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molecular phylogenetics evolution of molecules bioinformatics genomics population genetics molecular ecology BIOL 4041 BIOL 3046 BIOL 4041 BIOL 4010 BIOL 3042

BIOL 3042.03 Molecular Ecology

The analysis of molecular genetic data has revolutionized many areas of ecology and conservation biology. In support of this assertion, consider the following questions: How do you deduce parentage, kinship and mating patterns in wild populations from bits of fin, fur or feathers? Count bears (and other large mammals) with bits of fur? Identify the sex of mammals and the diet of sharks from fecal samples? Deduce population structures and average dispersal rates without tagging organisms? Use scale samples to tell whether the effective population sizes of fishes have changed

• ver the last few decades? Determine the continent and river of origin of Atlantic

salmon caught off Greenland? Compare the microbial diversity of deep seas vents and thermal hot spring? Identify the species and even population of origin of food products and consumer goods made from illegally harvested fish and wildlife? Determine where the ancestors of northwest Atlantic fishes spent the last ice age? This course will answer these and many other questions while introducing students to the methods and principles of the rapidly developing field of molecular ecology.

Pre requisites: BIOL 2030.03, BIOL 2060.03, STAT 2080.03 Co-requisites: BIOL 3041.03 or BIOL 2040.03 Exclusion: BIOL 4042.03 Instructors: P. Bentzen, D. Ruzzante Term: Winter

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Genes and Genomes: BIOL4010 / BIOC 4403 This class discusses the organization of genes into genomes. It deals with (i) compartmentalization of genetic material in nuclear and organellar genomes, (ii) the structure, behaviour and origins of components of both nuclear and organellar genomes which are not genes (transposable and other repetitive elements, introns), (iii) genetic and physical methods for mapping genomes, and (iv) the significance of genetic organization and higher order chromosomal structure and function. The methodology and prospects of the genomics will be discussed at some length. Bioinformatics: BIOL4041 / BIOC 4010 This class presents both the theoretical basis for, and the application of, computing in molecular biology and evolution. A wide range of topics will be addressed including the estimation of rates and patterns of mutations, sequence database searching, with an emphasis on phylogenetic analysis of genes and genomes. The content of the class may vary from year to year.

Laying the groundwork I: The birth of evolutionary theory Laying the groundwork II: A concise history of the gene Laying the groundwork III: Neo-Darwinism and the evolutionary synthesis

History

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Laying the groundwork I: The birth of evolutionary theory Darwin was not the first

1. The earth is young

• James Uscher: 4004 BCE
• 9:00AM Sunday 23 October to be exact

2. Species were immutable

• Species were created by God in exact forms

3. The value of science is to explain God’s creation

• Conflict with the church could be very bad for one’s career
• The rationalists began to set science in direct conflict with the

church

4. Imprecise knowledge of species

• Naming and organizing natural diversity was chaotic

Historical constraints to thoughts about nature of life on earth

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Carolus Linnaeus: I will name them all

• Carl van Linné (1707-1778), Swedish
• proponent of “Natural theology”
• set out to stop the chaos
• binomial nomenclature
• System Natura 1735 (142pp) Later editions

(>2300pp)

• rock star of field biologists
• believed species were immutable

Hutton: the world is older than you think

• James Hutton (1726-1797), Scottish
• did not like ad hoc explanations
• did not like “Catastrophism”
• champion of “Uniformitarianism”: the

present is the key to the past

• the Earth must be very old
• Hutton was a huge influence on Charles

Lyell (1797-1875) who wrote highly influential books on geology

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Lamarck: Species are not immutable

• Jean Baptist Lamarck (1744-1829), French
• first true museum systematist
• important work on patterns in fossil record
• first to put together two points:
• the world was very old
• species changed over this long time period
• Lamarck most famous for getting the

mechanism of evolution wrong (very sad)

• Lamarck and Erasmus Darwin

corresponded about evolution by acquired characteristics (Hmmm…)

Cuvier: Fossils are real

• Georges Cuvier (1769-1832), French
• father of comparative anatomy
• believed species were fixed.
• very influential and unkind to Lamarck
• convinced world that fossils were real
• must have seen same patterns in fossil

record as Lamark, seems he choose to ignore the implications

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Malthus: Life is a struggle

• Thomas Malthus (1766-1834), English
• political economist
• published “Essays on the principle of population”

(1790)

• Malthusian principle
• presented many examples of life as a struggle
• “profit of doom”
• Doctrine of Eugenics echoes back to Malthus

Young Darwin: I will voyage on the beagle

• Charles Robert Darwin (1809-1882), English
• started life as orthodox member of church
• naturalist on the Beagle
• observed many differences between species among

islands and between islands and mainland

• read Lyell while on voyage
• became a devout Uniformitarian; saw much evidence
• read Malthus two years after return to England; He

sees Malthus differently from all who came before

• drew info from very different sources; saw beyond the
• rthodox

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Older Darwin: I say species evolve by natural selection

1. Species produce more offspring than survive to age of reproduction. This leads to a “struggle”. 2. Food and other such resources are limited; more evidence for “struggle”. 3. Populations sizes surprisingly stable given the intensity of struggle among

• species. Must be a mechanism for stability.

4. Variation in the form of differences among individuals exists in every species. 5. Variation is heritable.

Ernst Mayr, in his book entitled “The Growth of Biological Thought” distils Darwin’s work to five key observations:

Older Darwin: I say species evolve by natural selection

1. Competition for finite resources ensures that many individuals within a species are eliminated because of inferior ability to survive and reproduce (low fitness). 2. Natural selection is the result of competition, where the more fit individuals

• utnumber the less fit individuals.

3. The characteristics favored by natural selection are passed on to succeeding generations because such characteristics are heritable.

From these observations, Darwin made three inferences: The consequences: all organisms must have descended, with modification, from common ancestors

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Wallace: Hey, I say so too!

• Alfred Russel Wallace (1823-1913), English
• full credit for “co-discovery” of evolution by natural

selection

• had epiphany while delirious from an attack of

malaria (1858)

• had read Malthus as well, and came to same

conclusion as Darwin Darwinian evolution fell into disrepute an languished until 1920’s Two problems that Darwin (and Wallace) could not solve: 1. Source of variation 2. Mechanism of inheritance

• Fleming Jenkin demolished Darwin in an article in the North British Review

(1876)

• Jenkins introduced the problem of “blending”