exam 2

DNA Substitution

A type of mutation where one nucleotide in the DNA sequence is replaced by another nucleotide.

Synonymous Substitution

A type of mutation that does not change the amino acid sequence of the protein.

Nonsynonymous Substitution

A mutation that results in a change in the amino acid sequence of the protein.

dN/dS Ratio

A measure used to distinguish between different evolutionary processes acting on genes, assessing the rate of nonsynonymous mutations (dN) compared to synonymous mutations (dS).

dN/dS = 1

Indicates neutral evolution (no selection).

dN/dS > 1

Indicates positive selection (favoring beneficial mutations).

dN/dS < 1

Indicates purifying selection (removing deleterious mutations).

Positive Selection

The process where favorable genetic variants increase in frequency in a population due to their advantageous traits.

Purifying Selection

The process that removes deleterious alleles from a population, thus conserving functionally important sequences.

Neutral Evolution

The hypothesis that most evolutionary changes at the molecular level are caused by random drift of mutant alleles that are selectively neutral.

Conservative Retention (Gene Duplication)

One gene copy retains the original function, while the other either becomes nonfunctional or develops a new function.

Neofunctionalization (Gene Duplication)

One of the duplicated genes acquires a new function that was not present in the ancestral gene.

Subfunctionalization (Gene Duplication)

Each duplicate gene retains a subset of the original gene's functions, thereby splitting the functional duties.

Maternal Effect Genes

Genes expressed in the mother that influence the development of the embryo, affecting traits like body axis formation.

Gap Genes

Segmentation genes that specify broad areas and lead to the formation of distinct body regions.

Pair Rule Genes

Segmentation genes that define pairs of segments in the embryo.

Segment Polarity Genes

Segmentation genes that establish anterior-posterior differences within individual segments.

Hox Genes

A group of related genes that control the body plan of the embryo along the head-tail axis, determining the identity of body parts.

Kimura’s Neutral Theory of Evolution

This theory posits that the majority of evolutionary changes at the molecular level are caused by random genetic drift rather than by natural selection.

Point Mutations

Changes at a single nucleotide position.

Single Mutations

Changes at a single nucleotide position.

Multiple Mutations

Changes occurring at multiple nucleotide positions simultaneously.

Coincident Mutations

Mutations that occur in two or more genes simultaneously.

Parallel Mutations

Independent mutations in different lineages that yield a similar trait.

Reversions (Back Mutations)

Mutations that revert a gene back to its original form.

Invisible Mutations

Mutations that do not affect the phenotype and thus are not subject to selection pressures. Generally, synonymous mutations tend to be invisible.

Homoplasies

Arise in cases where mutations occur independently in different lineages, leading to similar characteristics without common ancestry.

Morphological Species Concept

Defines species based on observable physical traits; commonly used for fossil species.

Biological Species Concept

Defines species as groups of interbreeding natural populations that are reproductively isolated from other such groups. Best for sexually reproducing organisms.

Lineage Species Concept

Species are defined as branches on the tree of life and are useful for asexual organisms and groups without clear reproductive boundaries.

Dobzhansky-Muller Model

A model of speciation that explains how genetic incompatibilities between diverging populations can arise. Hybrid offspring might inherit incompatible combinations of alleles, leading to reduced fitness.

Prezygotic Isolating Mechanisms

Mechanisms that occur before fertilization to prevent mating or fertilization (e.g., temporal, behavioral, mechanical isolation).

Postzygotic Isolating Mechanisms

Mechanisms that occur after fertilization that reduce the viability or fertility of hybrid offspring (e.g., hybrid inviability, hybrid sterility).

Hybrids

Offspring resulting from the mating of individuals from two different species.

Hybrid Zone

A geographic area where interbreeding occurs between two distinct species, often resulting in a mixture of genetic and phenotypic traits.

Ring Species

A connected series of neighboring populations that can interbreed with each other, but the populations at the ends of the ring cannot interbreed.

Allopatric Speciation

The formation of new species while geographically isolated from one another.

Sympatric Speciation

The formation of new species while sharing the same habitat.

Disruptive Selection

A type of selection that favors extreme phenotypes over intermediate phenotypes.

Polyploidy

A form of sympatric speciation that involves the duplication of chromosome sets, leading to organisms with more than two sets of chromosomes.

Autopolyploidy

A condition in which an organism has more than two sets of chromosomes all derived from a single species.

Allopolyploidy

A condition where two different species hybridize, and the resulting offspring have extra chromosome sets from both species.

Stratigraphy

The branch of geology concerned with the ordering and relative position of strata (rock layers) and their relationship to the geological time scale.

Radiometric Dating

A technique used to date materials such as rocks or carbon by measuring the radioactive decay of isotopes.

Radioisotopes

An isotope of an element that is unstable and can decay, releasing radiation.

Half Life

The time required for half of the radioactive atoms in a sample to decay (T_{1/2}).

Plate Tectonics

The scientific theory that explains the movement of the Earth's lithosphere which leads to geological phenomena such as earthquakes and the formation of mountains.

Mass Extinction

A significant and rapid decline in biodiversity on Earth, often marked by a high percentage of species loss within a relatively short time frame.

Permian/Triassic Mass Extinction Causes

Likely causes include volcanic eruptions, climate change, ocean acidification, and asteroid impacts.

Cretaceous/Paleogene Mass Extinction Causes

The leading hypothesis includes a massive asteroid impact (the Chicxulub crater) which led to drastic environmental changes.

Paleozoic Transitions

Highlights the evolution of fishes during the Devonian period and the subsequent colonization of land by both plants and animals.

Mesozoic Ecology

Saw the rise of dinosaurs and other reptiles as dominant terrestrial animal groups, along with significant