Evolution and Systematics Flashcards

Flashcards from lecture notes.

Theory

A testable explanation for a broad suite of observations that is supported by a lot of evidence/experiments (based on multiple lines of evidence and represents a complex body of knowledge).

Hypothesis

Single explanation/assumption made beforehand, based on observation or previous testing

Law

Descriptions of what happens under a specific set of conditions (often mathematical)

Logic

Application of logical rules for formulating general principles

Catastrophism

Sudden events (i.e. catastrophes) would change geological features and presence of species at a given time

Uniformitarianism

Geological features we see today are changing gradually through time and the processes causing that change are happening today

Laws vs. Theories

Statements about observed phenomena that consistently occur, whereas theories provide a framework for understanding those phenomena.

Experimental Thinking

Involved testing a hypothesis-was not as not as embraced as logic

Spontaneous Generation

Organisms arise from non-living matter spontaneously without any specific stimulus

Empedocles

One of the first thinkers to explain why species were different and lived in different places

Inheritance of Acquired Traits

An organism’s efforts during its lifetime causes changes to its phenotype, and these changes are passed to its offspring

Origin of Species

Published in 1859

Variation in the Population

Differences between individuals that can lead to higher reproductive success. These could be morphology, behavior, diet, etc.

Selective Agent

This could be any component that can change the chances of survival (predators, food, territory, etc.

Transformational Process

Each individual in the population changes (transforms) over its life-time

Variational Process

Sorting of pre-existing variation. Individuals are not changing through their lives, rather the frequencies of phenotypes in population change over generations by natural selection

Relevance of Finite Resources

resources are very limited in nature. This would spark the struggle for survival in the wild

Descent with Modification

Species split from common ancestor and slowly gain differences. This is why closely related species are similar (similar species on islands, and between islands and mainland)

Main Components of Natural Selection

Two main components are variation (that its heritable) and a selective agent (which produces differential reproductive success)

Variation Caused by Environmental Differences

Environment can cause phenotypic variation (the same genotype may produce different phenotypes under different environmental conditions-could lead to changes in reproductive success)

Fitness

A heritable trait that gives individuals a reproductive advantage will increase in frequency in a population

Life History

Refers to how organisms invest their energy in reproduction over their lifetimes

Natural Selection

Heritable Variation leads to differential reproductive success, process changes populations over time

Adaptation

A heritable trait that increases fitness in a certain environment was selected for its current function

Exaptation

A heritable trait that increases fitness in a certain environment but was originally selected for a different function but also advantageous

Convergent Evolution

Where similar traits (phenotype, behavior, etc.) can develop independently across very distant groups of organisms, as a result of similar selective pressures

Selection

Operates on the phenotype (size, behavior, toxins, proteins, etc.)

Inheritance

Phenotypic variants are associated with specific genotypes, which are inherited. Genes responsible for variation can be evaluated via common garden experiment, mating experiments, quantitative traits, etc.

Antagonistic Pleiotropy

A trait that increases fitness in one condition can decreases fitness in another setting

Phylogenies

Branching relationships of species, as they give rise to descendant groups over time. They can be based on morphological and/or genetic traits

Characters

Any observable or measurable characteristic of an organism

Traits

Represent the specific state of a character

Taxon (Taxa)

Groups represented at the tip of the branch

Root

Base of the tree, represents the common ancestor to all groups in the tree

Polytomy

When there is uncertainty in the relationships more than one branch will come out of one node

Cladogram

No branch lengths, just relationships

Phylogram

Branch lengths indicating some sort of evolutionary change (sequence divergence, phenotypic change, time, etc.

Monophyletic Group

A group formed by all the descendants of the most common ancestor and no additional members

Clade

Refers to group of species that share single recent common ancestor

Polyphyletic Group

When a group does not include the most common ancestor of all members, nor all the descendants from that ancestor

Paraphyletic Group

Contains the group’s most common ancestor but not all the descendants.

Rooted Trees

The ancestor from which all other lineages derive is included in the tree (can provide direction and sense of time)

Unrooted Trees

are not designed from the perspective of a single common ancestor (they do not provide a sense of direction or time and it is challenging to go from unrooted trees to rooted trees)

Analogy

Similarity in function or position between organs that have DIFFERENT evolutionary origin

Homology

Structures that have the same evolutionary origin, even if they have a different function.

Synapomorphy

Shared derived characteristic (Homology)

Homoplasy

Represents a trait that is similar between two species, but these two species do not share a common ancestor (Analogy)

Symplesiomorphy

Shared primitive characteristic that is not present or different in one of the species in the group

Vestigial Traits

Structures that were beneficial for an ancestor may no longer be necessary. They are reduced in size and their function is minimized over time

Maximum Parsimony

Among competing hypotheses, the tree with the fewest number of changes should be selected

Bootstrap Resampling

Sampling with replacement

Maximum Likelihood and Bayesian

Evaluate different trees (hypotheses) and determines their likelihood or probability based on a chosen evolutionary model

Gene

A sequence of DNA that specifies a functional product

Alleles

Variants of a gene

Locus

Location of a gene on a chromosome

Genotype

Combination of alleles that an individual has at a locus (or multiple loci). E.g., Aa

Phenotype

Observable characteristic of an organism. E.g., purple or white flowers

Law of Segregation

Each parent plant must contain two copies of the same gene, but they only pass one to their offspring (sexual reproduction)

Law of Independent Assortment

Alleles are passed down to the next generation in one locus, are independent of alleles passed down at another locus

Transcription

DNA is unwound by enzymes, and portions can be copied into RNA

Exon

DNA sequence that encodes for proteins

Introns

DNA stretches that do not code for proteins

Enhancers

Increase rate of transcription

Silencers

Decrease the rate of transcription

Cis Regulatory Elements

Same chromosome (nearby)

Trans RE

On different chromosomes

Mutations

Random changes in a DNA sequence of an organism (One of the main sources for genetic variation)

Somatic Mutations

Occur in the body of an organism are not passed to the next generation

Germ-Line Mutations

Associated with changes that can be transmitted to next generation

Synonymous Mutation

The new codon encodes the same amino acid; there is no change in the amino acid sequence

Nonsynonymous Mutation

The new codon encodes a different amino acid; there is a change in amino acid sequence

Frame Shift Mutation

Some mutations can lead to changes in the way DNA sequence is translated, when bases are inserted or omitted

Epigenetics

Changes in the process of DNA transcription, that DO NOT require changes in DNA sequence

Chromatin

Bundles of DNA strands coiled in proteins called histones

DNA Methylation

Involves the addition of a Methyl group to the DNA, changing the ability to bind to transcription factors

Hardy-Weinberg Model

Null model that allows us to understand what happens when external forces (e.g. selection, assortative mating, etc.) are not operating

Directional Selection

One allele is consistently favored over the other. Frequency of the favored allele increases in the population

Overdominance

Heterozygote has higher fitness than either homozygote.

Underdominance

Heterozygous has lower fitness than either homozygotes

Frequency-Dependent Selection

The fitness of a phenotype depends on the frequency

Positive Frequency-Dependent Selection

Fitness of a phenotype increases as frequency increases in a population

Negative Frequency-Dependent Selection

Fitness of phenotype decreases as the frequency of the phenotype increases

Assortative Mating

Individuals tend to mate with others of the same genotype or phenotype (fast accumulation of homozygous genotypes in population)

Disassortative Mating

Individuals tend to mate with others of different genotypes or phenotypes

Inbreeding Depression

Offspring of genetic relatives have reduced fitness because of the accumulation of deleterious recessive alleles

Genetic Drift

Evolution due to chance events in small populations (change in allele frequency due to sampling error)

Coalescence

The process by which a lineage converges on a single genotype over time

Bottleneck

A very large population can be dramatically reduced in a short period of time. Alleles are lost due to an accelerated pace of genetic drift in a smaller population

Founder Effect

A specific case of genetic drift. It occurs when a small group of individuals becomes isolated or separated from a larger population to form a new, isolated population.

Haldane’s Rule

A new beneficial mutation might not be fixed if it is in a small proportion of the Ne. This is because drift can easily remove it

Neutral Theory of Evolution

Analyzing molecular data directly can help us detect differences in DNA, RNA or amino acid sequences between populations, even when there are no obvious phenotypic differences

Polygenic Traits

Traits that are affected by many genes simultaneously

Latent Variation

When many genes affect a trait, where are so many possible genotypes that many combinations of alleles are not observed in nature

Epistasis

Alleles at multiple loci interact in nonadditive ways to determine phenotypes

Linkage Disequilibrium

This represents the non-random association of alleles that are present in different loci

Genetic Hitchhiking

During selective sweeps… neutral or mildly deleterious alleles increase in frequency when in linkage disequilibrium with a beneficial allele

Quantitative Trait

A trait that has continuous variation

Broad Sense Heritability

Total variance in a trait that is due to genotype is defined as

Narrow Sense Heritability

The proportion of variation that is due to additive genetic effects alone.

C-Value Paradox

The size of the genome does not correlate well with the observed “complexity”