Genomics, Bioinformatics, and Evolutionary Biology: Key Concepts and Definitions

Genomics

the study of whole sets of genes and their interactions

Bioinformatics

the application (data mining) of computational methods to the storage and analysis of biological data

Proteomics

the systematic study of the full protein sets expressed by cells

Proteomes

full protein sets

Systems biology

aims to model the dynamic behavior of whole biological systems based on the study of interactions among the system's parts

Evolutionary Developmental Biology (evo-devo)

a field of study that investigates the interplay between evolutionary and developmental processes

Gene density

number of genes, in a given length of DNA

Human non-coding DNA

does not code for proteins, rRNAs, or tRNAs (has no effect on life)

How much of human DNA is noncoding

98.5%

Gene fragments

unique noncoding sequence

Pseudogenes

former genes that have accumulated mutations and are now nonfunctional

Repetitive DNA

present in multiple copies in the genome

Genome

mapping of all genes (location, sequence)

What is the purpose of comparing genomes

understanding/identifying evolutionary relationships

Highly conserved genes

remained similar over time

Comparative genetics

a form of study to confirm the relevance of research on model organisms to our understanding of biology in general and human biology in particular

Single nucleotide polymorphism (SNPs)

1 ATCG change

Most variations within humans are due to

single-nucleotide polymorphisms (SNPs)

What happens when a location's food increases

population increases

Uniformitarianism

countless small changes over vast periods of time

Evolution

can be defined by Darwin's phrase "descent with modification," and can be viewed as both a pattern and a process

Descent with modification

this concept explains how, with natural selection, the adaptations of organisms and the unity of a diverse life

natural selection

a process in which individuals with favorable inherited traits are more likely to survive and reproduce

Immutable

unable to be changed

Homology

similarity resulting from common ancestry

homologous structures

anatomical resemblances that represent variations on a structural theme present in a common ancestor

Vestigial structures

remnants of features that served important functions in the organism's ancestors

Convergent evolution

the evolution of similar/analogous features in distantly related groups

Analogous

similar or showing a partial similarity that allows for comparison between two otherwise different things

Fossils

remains or traces of organisms from the past

Strata

layers of sedimentary rock that hold fossils

Paleontology

the study of fossils

Biogeography

the scientific study of the geographic distribution of species

Endemic

species that are not found anywhere else in the world (ex, species specific to islands)

What does natural selection act on

individuals

artificial selection

a process by which species are modified by selecting and breeding individuals with desired traits

Individuals with certain heritable traits can

survive and reproduce at a higher rate

Evolutions by natural selection involve

chance and sorting

Traits that are adaptive will

vary with different environments

natural selection increases

the frequency of adaptations

Divergent species share

a common ancestor (and have diverged from one another over time)

Changes in life can be explained through

natural selection

Adaptive evolution

an increase in the frequency of an allele that improves fitness by acting on an organism's phenotype

Main example of adaptations

camouflage

Key role of natural selection in adaptive evolution

increases the frequency of alleles that enhance survival and reproduction

Relative fitness

the contribution an individual makes to the gene pool of the next generation, relative to the contributions of other individuals

Microevolution

change in allele frequencies in a population over generations (leads to genetic variation)

genetic variation

difference among individuals in the composition of their genes or other DNA sequences

Gene duplication

alterations in the number or position

Gene variability

genetic variation at the whole gene level, which can be quantified as the average percent of the heterozygous loci

Natural selection can only act on

phenotypic variation that has a genetic component

Pseudogene

nonfunctional gene

Neutral variation

differences that do not confer a selective advantage or disadvantage

What is genetic drift driven by

chance

Genetic drift

variation in the relative frequency of different genotypes in a small population

Circumstances that result in genetic drift

founder effect and bottleneck effect

Founder effect

when a few individuals become isolated from a larger population, and the smaller group establishes a new population

Bottleneck effect

can result from a drastic reduction in population size due to a sudden environmental change

Gene flow

the movement of alleles among populations

How does gene flow happen

through gametes

What does gene flow do

reduce genetic variation between populations over time and affect the fitness of a population (increase or decrease it)

What does the Hardy-Weinberg equation describe

the genetic makeup expected for a population that is not evolving (describes the constant frequency of an allele in a gene pool)

Law

proven mathematically

Theory

widely accepted

Population

a localized group of individuals capable of interbreeding and producing fertile offspring

Gene pool

all the alleles for all loci in a population (variety of genes in a species)

Allele frequency

the relative frequency of an allele at a particular locus

Allele

a variant of a gene

Gametes

mating between populations

Balancing selections

occurs when natural selection maintains stable frequencies of two or more phenotypic forms in a population, keeping the frequency of each phenotype close to 50%

Heterozygote advantage

when heterozygotes have a higher fitness than do both homozygotes

Frequency-dependent selection

when the fitness of a phenotype depends on how common it is in the population

Sexual selection

natural selection for mating success

Sexual dimorphism

marked differences between the sexes in secondary sexual characteristics

Intersexual selection

members of one sex choose the opposite sex

Intrasexual selection

competition among individuals of one sex (often males) for mates of the opposite sex

Speciation

the process by which one species splits into two or more species

Microevolution

changes in allele frequency in a population over time

Macroevolution

broad patterns of evolutionary change above the species level

Reproductive isolation

the existence of biological barriers that impede two species from producing viable, fertile offspring

Hybrids

offspring of crosses between different species

Prezygotic reproductive barrier

blocks fertilization from happening

Habitat isolation (type of prezygotic reproductive barrier)

two species encounter each other rarely, or not at all, because they occupy different habitats, even though not isolated by physical barriers

Temporal isolation (type of prezygotic reproductive barrier)

species that breed at different times of the day, different seasons, or different years cannot mix their gametes

Behavioral isolation (type of prezygotic reproductive barrier)

courtship rituals and other behaviors unique to a species are effective barriers

Mechanical isolation (type of prezygotic reproductive barrier)

morphological differences that prevent successful mating

Gametic isolation (type of prezygotic reproductive barrier)

sperm of one species may not be able to fertilize eggs of another species

Postzygotic reproductive barrier

prevents the hybrid zygote from developing into a viable, fertile adult

Reduced hybrid viability

genes of the different parent species may interact and impair the hybrid's development or survival

Reduced hybrid fertility

even if hybrids are vigorous, they may be sterile

Hybrid breakdown

Some first-generation hybrids are fertile, but when they mate with another species or with either parent species, the offspring of the next generation are feeble or sterile

Morphological species concept

defines a species by structural features

Ecological species concept

views a species in terms of its ecological niche

Phylogenetic species concept

defines a species as the smallest group of individuals that share a common ancestor, a single branch on a phylogenetic tree

Sympatric speciation

takes place in species that live in the same geographic area

Polyploidy

the presence of extra sets of chromosomes due to accidents during cell division

Autoploidy (ex of polyploidy)

an individual with more than two chromosome sets, derived from one species

Allopolyploid (example of polyploidy)

a species with multiple sets of chromosomes derived from different species

Habitat differentiation

the appearance of new ecological niches

Hybrid zone

a region in which members of different species mate and produce hybrids