BIO 203 Q6

Biological Species Concept (BSC)

A species is a group of organisms that can interbreed and produce viable, fertile offspring, and are reproductively isolated from other such groups. 

• Populations united by gene flow are the same species

• Cannot be used for fossils or extinct organisms

• Cannot be used for animals that do not do sexual reproduction

• Invalidated by some hybrids

Reproductive Isolation

Biological barriers that prevent two species from producing viable, fertile offspring. 

Allopatric Speciation

Formation of new species due to geographic separation of populations. 

• Also colonization of a new territory by some members of a population

Parapatric Speciation

Speciation occurring when populations are adjacent but experience different selective pressures and limited gene flow. 

• No specific barrier to gene flow but there is still non-random mating

Sympatric Speciation

Speciation that occurs without geographic separation, often through ecological, behavioral, or genetic isolation within the same area. 

• Species diverge within the same geographic area

Prezygotic barriers

Barriers that prevent mating or fertilization from occurring.  

• Behavioral Isolation: Differences in mating behaviors prevent interbreeding. 

• Gametic Isolation: Sperm of one species cannot fertilize eggs of another species. 

• Geographic Isolation: Physical separation of populations by barriers (e.g., mountains, rivers). 

• Habitat Isolation: Species live in the same area but in different habitats and do not meet. 

• Mechanical Isolation: Incompatible reproductive structures prevent successful mating. 

• Temporal Isolation: Mating occurs at different times (e.g., seasons or time of day). 

Postzygotic barriers

Barriers that occur after fertilization, preventing viable or fertile offspring.  

• Hybrid Breakdown: Offspring of hybrids are weak or sterile in subsequent generations. 

• Hybrid Inviability: Zygote or embryo fails to develop or survive to reproductive age. 

• Hybrid Sterility: Hybrid offspring are sterile and cannot reproduce (e.g., mule). 

Most Recent Common Ancestor (MRCA)

The most recent individual from which all organisms in a group are directly descended. 

• Monophyletic group contains all the descendants from MRCA

• Paraphyletic group does not contain all descendants from MRCA, only ones with a shared primitive character state

Phylogenetic Tree

A diagram showing evolutionary relationships among species based on shared ancestry. 

Clade

A group consisting of an ancestor and all its descendants; a monophyletic group. 

• Ba e shared derived characteristics - either morphological or molecular

• If a common ancestor is found, everything following will be in a clade

Parsimony

The principle that the simplest explanation (requiring the fewest evolutionary changes) is preferred when constructing phylogenies. 

• No preference for gains vs losses

Exaptation

Traits that were originally selected for one function but were later co-opted to serve a different, selectively advantageous function.  

Divergent evolution

process by which two or more species that share a common ancestor become increasingly different over time

• Typically due to adaptation to different environments or ecological niches

• Often leads to homologous structures, which are traits that have the same evolutionary origin but different functions  

Convergent evolution

Processes of independent evolution of similar structures in unrelated species. Also known as homoplasmy  

• Natural selection works in similar ways on multiple taxa

Homologous Trait

A trait inherited from a common ancestor (e.g., forelimb bones in vertebrates). 

Analogous Trait

A trait that evolved independently in different lineages due to similar selective pressures (e.g., wings in bats and insects). 

• Natural selection operated in similar ways

Bootstrapping

A statistical method in phylogenetics to assess the reliability of tree branches by resampling the data and recalculating the tree many times. 

• Provides a measure of internal consistency of the pattern of common ancestry 

Node

hypothetical common ancestors whose traits were likely passed down

Next generation sequencing

determines the sequence of a single DNA strand by complementary strand synthesis

• Detects which nucleotide is added at each step

• Faster and cheaper

• Can sequence multiple fragments at once

• Does NOT use chain termination, unlike dideoxy sequencing

Interspecific comparisons

identify sequences conserved over evolutionary time

• Based on comparisons between species 

Intraspecific comparisons

identify sequence polymorphisms responsible for genetic differences among individuals of a single species 

Homologs (homologous genes)

are genes that descended from a common ancestral gene and constitute a gene family 

• Comparison of homologous nucleotide alignment can be used to understand phylogenetic relationships

Paralogs (paralogous genes)

are genes that originated by a duplication event; generally they perform biologically distinct, but biochemically related, functions 

Orthologs (orthologous genes)

Genes in different species that are derived from a single ancestral gene in the species’ last common ancestor 

• Often have equivalent functions in the two organisms being compared

Mechanisms for molecular evolution

• Mutation within a gene

• Mutation within a regulatory region

• Gene duplication and divergence

• Exon shuffling

Gene Duplication

Duplication of a region of DNA that contains a gene

• In evolutionary terms, mutations of the genes can lead to divergence of the gene products leading to new gene function 

• If the entire gene is duplicated, one copy can be free to evolve new functions

Fate of gene duplication

• Pseudogene: duplicate accumulates a mutation and is nonfunctional

• Subfunctionalization: mutations in each of the two copies of a gene creates genes with complementary functions

• Neofunctionalization: mutation in one of the copies provides a new function

Exon shuffling

Process through which two or more exons from different genes can be brought together in the genome 

• Exons can swap intron regions and get spliced into existing exons

• Very rare event

Deleterious Mutation

A genetic change that reduces an organism’s fitness (ability to survive and reproduce)

• Natural selection typically acts against deleterious mutations. 

Neutral Mutation

A genetic change that has no effect on an organism’s fitness. These mutations are not affected by natural selection and typically evolve through genetic drift.

• Ex. synonymous change, change in non-coding region, nonsynonymous change that does not alter protein function 

Beneficial Mutation

A genetic change that increases an organism’s fitness. Natural selection tends to favor these mutations, leading them to spread in the population. 

Synonymous mutation

A DNA mutation that does not change the amino acid sequence of the protein because of the redundancy in the genetic code

• Silent mutation

Nonsynonymous mutation

A DNA mutation that does change the amino acid sequence of the protein. 

• Missense mutation

Neutral theory

there should be no difference in the number of synonymous and nonsynonymous if neutral selection is occuring

• Deviations from this can be used to determine the type of selection occurring

• pN/pS = dN/dS

• dN = nonsynonymous substitutions / nonsynonymous sites (different species, fixed) 

• dS = synonymous substitutions / synonymous sites (different species, fixed) 

• pN = nonsynonymous substitutions / nonsynonymous sites (within species, polymorphisms) 

• pS = synonymous substitutions / synonymous sites (within species, polymorphisms) 

Molecular Clock

A concept in evolutionary biology that uses the rate of molecular change (such as DNA mutations) to estimate the time of divergence between species or lineages. 

Purifying (negative) selection

Fewer nonsynonymous changes than expected 

• pN/pS > dN/dS < 1

• Removes harmful mutations

• Maintains the current common allele

• Nonsynonymous substitutions will be rare relative to synonymous

Neutral selection

No selection (pN/pS  ~  dN/dS ~ 1) 

Positive selection

More nonsynonymous changes than expected

• pN/pS < dN/dS > 1

• Favors advantageous changes 

• Nonsynonymous mutations will occur more rapidly than synonymous due to drift