Evolutionary Biology Unit 1

emipirical approach

1. Studying the fossils record-provide a record of evolution. •Fossil evidence shows change in forms over time. •Fossils of simpler organisms are found in older rocks, newer rocks contain more complex organisms. •New fossils found many time fill in "gaps" (transitional forms) •The age of fossils found in sedimentary rocks can be determined using radioactive decay. 2. Geographic distribution of living things = Beaver in North America and Capybara in South America are closely-related species but living in different places. With time they have evolved and look different-Divergent evolution. = While Beaver and Muskrat are distantly-related species but are exposed to similar pressure of natural selection. They many ended up in evolving similar characters-Convergent evolution. 3.Studying the comparative morphology -homologous and analogous structures 4. Studying of comparative embryology.Similarities in embryos showed relationships between common ancestor 5. Molecular homology DNA sequence analysis-more closely related have more similar DNA

Components of natural selection

1. Variation 2. Inheritance 3. Differential reproductive success

theories of geological change

1. catastrophism 2. gradualism 3. uniformitarianism

pedigree vs phylogeny

A pedigree tells us about the ancestry of individuals, whereas phylogenies tells us about the ancestry of the populations. A pedigree tend to expand as one look backward in time, in contrast phylogeny expands as we move forward in time.

homoplasy

A similar (analogous) structure or molecular sequence that has evolved independently in two species.

bootstrap resampling

A statistical technique for quantifying how strongly a data set supports a given phylogeny.

phylogenetic diversity

- All living things have descended from a common ancestor. - Over millions of years this common ancestor evolve and diversify to myriads of forms.

evolutionary biology

- Allows us to infer the relationships among all life that has ever lived. - Track the diversity of life across vast stretches of time. - Test hypotheses with observation and experiments.

Processes responsible for modification

- Natural selection one of the most important processes responsible for modifications that occur over time. - Phenotype: the observable, measurable characteristics of organism. - Mutations: Change to the sequence of the DNA - Fitness: is measured in terms of relative survival rates and reproductive success - Mutation can increase fitness, decrease fitness or have no effect in fitness - Accumulation of advantageous genetic changes over the long periods of time can produce a dramatic effect--species, genera, families and higher taxonomic order.

methods for building trees

- parsimony -distant methods -maximum likelihood -Bayesian inference

parsimony

-The easiest ones to explain, and were also among the first methods for inferring phylogenies. -The goal is to identify that phylogeny that requires the fewest necessary changesto explain the differences among the observed character.

phylogenetic tree uses

-To understand lineage of various species -To understand how various functions evolved

distance method

-We measure the pairwise distances between the species and then use these distances to reconstruct a tree. -It is measurement of morphological or genetic differences between species -Here distances are calculated by tallying the number of character differences between species.

evolution

-a process by which different kinds of living organisms are thought to have developed and diversified from earlier forms during the history of the earth. -The study of the origin, maintenance, and diversity of life.

mutation

-is one of the major sources generating the variation on which natural selection acts. -occurs at random, independently whether they would be favored by natural selection or not.

Macroevolution

-the long-term accumulation of small changes in gene frequency within a species. -Over time, these genetic differences become so pronounced that the population undergoing the shift can no longer breed with the ancestral group.

Linnaeus

He developed both a binomial system for naming organisms and a hierarchy of classification groupings. He was the father of taxonomy. He had insight that organisms can be organized into a hierarchical system of classification without having a theoretical explanation for why these patterns should exist.

Empedocles (492-432 BC)

He had come up with a sort of evolutionary theory: past natural selection is responsible for the forms we see today.

theoretical approach

In evolutionary biology, theory plays an important role. Often time involves creating mathematical models of the biological system Most population geneticists uses variety of mathematical models to explain the appearance of new alleles, new genotypes and changes in the existing alleles and genotypes .

Why do many species-humans included-exhibit an even ratio of one male to one female?

In most species, a single male can fertilize numerous females, and often male does not provide nothing towards the care of the offspring. Why could there not be an excess of females and the ratio is biased towards female?

Linnaen taxonomy

Linnaeus developed both a binomial system for naming organism and a hierarchy of classification groupings without a theoretical basis for hierarchical patterns Kingdom, Phylum, Class, Order, Family, Genus, Species

Darwin on common ancestry

All living creatures drive from one or few common ancestors. Just like artificial selection can create multiple new varieties from a single domesticated variety. Similarly natural selection, over the time generate multiple new species from an ancestor

problems with Darwin's theory

Problem 1: Accounting for complex structures with Multiple intricate parts Problem 2: Explaining traits that appear to lack any biological function Problem 3: Why does variation persists in the face of natural selection?

Catastrophism

Cuvier proposed the natural disasters have happened often during Earth's long history These events shaped landforms and caused species to go extinct. The newly created species replaced the extinct ones.

Darwin's theory

Darwin presented two great laws to explain the process of evolution. Natural Selection -Organisms with favorable traits survive, reproduce, and pass the variations to the next generation. Descent with Modification-all species have descended from one or a few common ancestors. The species that share a recent common ancestor tend to resemble one another in many respects

Erasamus Darwin

Darwin's grandfather" would it would be bold to imagine...that all warm-blooded animals have arisen from one living filament.

Lamarck

Developed a "transformation" theory for evolutionary change in his Zoological Philosophy in 1809 (same year Darwin was born). The use and disuse of body parts leads to their development or deterioration. The acquired characteristics can be inherited Driven by need

synapomorphy

When the derived trait is shared because of common ancestry, we call it a shared derived trait

unrooted tree

a phylogenetic diagram which lacks a common ancestor or a basal node. This type of a tree does not indicate the origin of evolution of the groups of interest. It depicts only the relationship between organisms irrespective of the direction of the evolutionary time line.

polyphyletic group

a set of organisms that have been grouped together but do not share an immediate common ancestor.

outgroup

a taxon that is related to the group of interest but which branched off earlier in evolutionary history

co-option

a trait to serve a new function of purpose-intermediate stages of complex traits were functional and selected, but they did not serve the same function in the past as they do today.

common ancestry

all living creatures derive from one or few common ancestors, and descent with modification would generate nested hierarchies.

tree of life (phylogenic tree)

all species that live as forming a vast branching tree of relationships

cladistic analysis

an approach to biological classification in which organisms are categorized based on shared derived characteristics.

Monophyletic group

set of organisms that forms a clade, which consists of all the descendants of a common ancestor. typically characterized by shared derived characteristics.

symplesiomorphy

shared ancestral trait

Analogous trait

shared by two or more species, not because of history of common descent, but because of some evolutionary process, like natural selection, has independently fashioned similar traits in each species

Homologous Structures

similar morphology, even if function is different, indicates a close evolutionary relationship.

chronogram

branch length represent actual time rather than amount of evolutionary change.

Exaptations

some traits were originally selected for one function but later co-opted to serve different, advantageous functions

life history strategy

can refer as a life table of an organism, and can be imagined as various investments in growth, reproduction, and survivorship.

natural selection

cause: environment speed of change: slow reason for selection: the selected traits improves the organism's chances of surviving and reproducing effect on fitness: improves fitness (although only for the circumstances in which it is selected. If conditions change, the selected trait may no longer be advantageous)

artificial selection

cause: humans speed of change: fast reason for selection: the trait is desirable to human breeders effect on fitness: often causes decrease in fitness

phylogeny

the history of the evolution of a species or group, especially in reference to lines of descent. In other word, the branching relationships of a population as they give rise to multiple descendant population over time. can based on anatomical features, morphological trait, behavioral pattern, developmental processes or genetic sequences.

Analogous Structures

demonstrate organisms are not related evolutionarily -similar function, different morphology.

Redi's experiment

demonstrated that maggots did not arise through spontaneous generation. Uncovered jars with meat have fly eggs and maggots. When the jars are covered, and flies cannot enter and lay eggs on the meat, no eggs or maggots are found.

norm of reaction

describes the pattern of phenotypic expression of a single genotype across a range of environments. One can use reaction of norms with differing genotypes within a single species to a particular phenotypic trait and environment variable.

systematics

the study of the biological diversity in an evolutionary concept.

branch length

the time or degree of genetic change in a lineage

Homologous trait

traits that are similar to one another due to shared ancestry. As species adapt to their environments and evolve over time, these traits may change in appearance and in function, but ultimately they still share the structure, genetics, or embryonic structure of their common ancestor.

Tiktaalik

transitional fossil between fish and tetrapods new forms of locomotion, respiration, and hearing flat body, eyes on top of flattened head, robust pectoral and pelvic girdles, limb-like fin appendages

phylogram

trees with evolutionary change with the branch length. Branches are of different length. Convey amount of evolutionary change along the branch of the tree.

polytomy

uncertainty in phylogenetic relationships

descent with modification

each living species has descended, with changes, from other species over time

taxon

each tip of phylogenetic tree represents a group of related organisms rotating around any node doesn't affect phylogeny

mythology

every human culture has nurtured a set of creation myths to explain how the world was created

phylogenetic diagram (cladogram)

uses lines that branch off in different directions ending at a clade, a groups of organisms with a last common ancestor. These branching off points represent a hypothetical ancestor (not an actual entity) which can be inferred to exhibit the traits shared among the terminal taxa above it.

pairwise distances

final estimates of the difference between all possible pairs of sequences

law of succession

groups of fossils appear in a chronological order through their vertical placement in sedimentary rocks. In the same way that the oldest rocks are found in the bottom layer of the earth, the oldest fossils also followed the same chronology as they appear in the same set of rock layers, or strata.

bootstrap support

numbers at a branch point

Convergent evolution

occurs when two or more species become similar to one another because they are exposed to similar selective conditions.

Fisherian Sex Ratio Theory

predicts that selection will lead to equal investment in male and female offspring. If sons and daughters take the same investment in resources to produce each individual offspring, the population sex ratio should be 50:50. This prediction of equal investment holds true regardless of the breeding structure of the population(e.g. monogamy vs. polygamy) or whether one gender has a greater chance of survival than the other. If sex ratio falls below 50%, increased production of rare sex is favored.

Anaximander (610-546 BC)

proposed a mechanistic view of the earth and heaven where the laws of physics replace the supernatural way of creation

gene duplication

provides a way of evolutionary diversity in which a protein can switch/gain/loss/conserve function.

vestigial trait

remnant of a structure that may have had an important function in a species' ancestors, but has no clear function in the modern species.

interior nodes

represent common ancestors

Aristotle (384-322 BC)

The Greek philosopher that wrote in his "Natural history of animals", Principle must agree with facts or we need to rethink. This sort of approach was beginning of modern evolutionary biology and biologist. However, he sometimes did not follow his own rule, because he once proposed that women had fewer teeth than men and maintained his view.

biological diversity

The variety and complexity of species present and interacting in an ecosystem and the relative abundance of each.

Pasteur's experiment

This has all of the hallmarks of modern scientific inquiry. It begins with a hypothesis and it tests that hypothesis using a carefully controlled experiment.

Spontaneous Generation (Abiogenesis)

•First proposed by Aristotle that living organisms are generated from non living things. •Flooding of Nile river left muddy soil followed by emergence of frogs. Conclusion : frog come from muddy soil •That time people use to believe that mice spontaneously appear in stored grain or maggots spontaneously appear in rotten meat.

traits on a tree

•Fossils •Embryological processes •Behavioral patterns •Morphological data •Chromosome structure •DNA sequences

life history strategy traits

•Size at birth •Growth pattern •Age and size at maturity •Number, and sex ratio of offspring •Timing of ageing and senescence

Summary of Darwin's theory

=Genetic variation: variety exists among individual of a species =Overproduction: More individuals are born than survive to reproduce =Struggle for existence :Organism compete for resources, struggle for existence. =Differential survival and reproduction: Organisms with advantages survive and pass those advantages to their children =Gradual change: if characteristics are inherited, species slowly evolve =Species alive today have descended with modification from species that lived in the past. =All the organisms on earth are united into single tree of life.

shared derived characters

Characters that recently appeared in lineage not in the older members.

uniformitarianism

Charles Lyell expanded Hutton's idea of gradualismin to the theory of uniformitarianism. Said changes in Earth occurred at constant rate over time. Those changes we see happening today. Based his theory on fossil deposits.

how to root a tree

Finding the midpoint or distance -The midpoint of the most distant two taxa in the tree can be assumed as a root for the phylogenetic tree. Finding an outgroup -This requires prior knowledge about the relationships between taxa. Then a taxon which lies outside the group can be used as an outgroup to draw a rooted phylogenetic tree.

Gradualism

Hutton's concept that changes on earth has occurred in small steps over long period of time

conservation biology

If we try to preserve evolutionary history, the loss of the single species—which represents the only species on its branch of our tree—would produce a deeper cut than the loss of all the species in a hot zone where speciation is occurring rapidly.

Buffon

Origin of Earth: comet striking the sun had broken off debris that became the planets of the solar system. Initially, the Earth was scorching, but gradually it cooled until molten rock turned to dry land and clouds rained down to form oceans. He estimated the entire process took over 70,000 years. To most Europeans of his time, who considered the Earth to be fewer than 7,000 years old. Change through migration: he believed that modern Indian and African elephants were migratory descendants of Siberian mammoths.

Divergent evolution

Phenomenon in which initially similar populations accumulate differences over evolutionary time, and so become increasingly distinct .

Microevolution

Small scale changes within a species to produce new varieties or species in a relatively short amount of time.

human vs natural selection

Sometime natural selection work against artificial selection. •For example: In most selective breeding program the farmers focus to the improving the quality and yield of the crop. They didn't target on resistance to insect damage. •Human develop pesticide thus reducing crop pests and thereby increasing crop productivity. •In this scenario, natural selection generally favors crop pests that are most resistant to pesticide.

genetic engineering

The manipulation of genetic material for human purposes, a practice called genetic engineering or in a broader term biotechnology. The basic idea behind genetic engineering is to put a gene of interest -that produces a useful protein of trait into another piece of DNA to create recombinant DNA. So it is DNA combined from two or more sources. Genetic engineering has been used to produce hormones, treatment of humans, increase food production from plants and animals and gain insight into growth processing of cells and organisms.

cladogram

a diagram that shows the evolutionary relationship among a group of organisms. These trees do not have different branch length. All branch length aligned. Convey only the pattern of relationships .

variation

a difference in a physical trait.

paraphyletic group

a group of organisms that contains a common ancestor and only some of the descendants of that ancestor.

trade-off

When evolution increases one life history characteristic, frequently another characteristic may decrease

phylogenetic tree

a hypothesis about the evolutionary history.

Weismann

cut the tails off of mice & proved that acquired characteristics were NOT inherited