Unit I Concepts: An Idea that Changed the World; The Tree of Life; Natural Selection and Adaptation

proximate; ultimate (evolutionary)

two kinds of “why” in evolution

proximate causation

explains how the trait works or develops; is immediate— observed within the lifetime of the individual; involves physiology, hormones, anatomy, genes, development, and learning

ultimate (evolutionary) causation

explains why the trait exists— its evolutionary history and function; explores a historical time frame over generations; involves natural selection and other evolutionary processes acting on ancestors

hypothesis

a testable, provisional explanation; it must be capable of being shown wrong

fact

an observation or conclusion confirmed so thoroughly that it is provisionally accepted;

scientific fact

the status of evolution, with regards to public perception

theory

a comprehensive, well-supported framework that explains many facts and has survived repeated testing; not a guess

mutation; selection; drift; gene flow

the four theorized causes of evolution; causes change in allele frequencies

evolution

inherited change in the properties of groups of organisms (populations) over the course of generations; observed in groups, not individuals; inherited; not necessarily adaptive; involves change in allele frequencies; descent with modification

anagenesis; cladogenesis

two types of observed changes for lineages

anagenesis

change within a single lineage over time

cladogenesis

the splitting of one lineage into two or more

microevolution; macroevolution

two types of evolution

microevolution

change within populations and species

macroevolution

the origin of new species and higher taxa; the long-term accumulation and extension of microevolutionary processes; gradual change within species, continued over long periods

Great Chain of Being (scala naturae)

a fixed, linear ladder of permanent, individually created forms from “lowest” to “highest”; species do not change and organisms are ranked

Darwin’s tree

branching descent with no built-in ranking and no requirement of increasing complexity

Carolus Linnaeus

a Swedish biologist regarded as the Father of Modern Taxonomy; classified species into nested groups; relatedness meant nearness in the Creator’s design, a pattern of similarity

Darwin’s relatedness

recency of common ancestry; nested hierarchy is reinterpreted as genealogy

Charles Lyell

a Scottish geologist who popularized the theory of uniformitarianism, stating that Earth's geological features were formed by slow, natural, and continuous processes over vast periods

uniformitarianism

the same slow processes operating today operated in the past, so an ancient Earth could accumulate large changes gradually; gave Darwin the concept of deep time and gradual change

Jean-Baptiste Lamarck

proposed that species change through time; organisms change by use and disuse of parts in response to needs, and the acquired changes are passed to offspring (inheritance of acquired characteristics)

Lamarckian source of change

individuals change during life through need, use, and disues

Darwinian source of change

individuals already differ; variation exists before selection

Lamarckian heredity

acquired changes are inherited

Darwinian heredity

only heritable variation matters; changes acquired during life are not inherited

Lamarckian mechanism

direct, adaptive modification of individuals, then transmission

Darwinian mechanism

differential survival and reproduction of variants

Lamarckian direction

driven by need or by an inherent tendency toward complexity

Darwinian direction

no foresight; adaptation to current conditions

individuals

what changes according to Lamarck’s view of evolution

population composition

what changes according to Darwin’s view of evolution

Alfred Wallace

an English naturalist and explorer; independently proposed natural selection as the mechanism of evolution with Darwin

natural selection

organisms produce more offspring than can survive; individuals vary; some variation is heritable; variants differ in survival and reproduction; therefore heritable traits that improve reproductive success increase in frequency

artificial selection

demonstrated that selection on heritable variation produces change; nature acts similarly but without a conscious agent

Thomas Malthus

contributed the idea that populations tend to outgrow their resources, which produces a struggle for existence

blending inheritance

a gap in Darwin’s understanding of the theory of inheritance; in which offspring are an average of their parents; variation is diluted every generation, eliminating the raw material that selection needs

particulate (Mendelian) inheritance

keeps discrete hereditary factors intact, so variation is preserved; initially conflicted with gradual selection; combined with Darwinism in the synthesis

neo-Lamarckism

acquired characteristics are inherited; the environment or use directs adaptive change; main weakness is that there is no evidence that mutations are induced in the advantageous direction

August Weismann

debunked neo-Lamarckism through the mouse tail experiment; separated the body from the hereditary germ line and cut off mouse tails for many generations with no effect on descendants

orthogenesis

an internal drive pushes lineages along fixed, straight-line trends, regardless of adaptive value; however, no mechanism was ever proposed, and trends in the fossil record can be explained by selection and history and need not be adaptive

mutationsim

the theory that new species (and higher taxa) arise suddenly by single large mutations; mutation, not selection, is the creative force

mutation

is the raw material that selection sorts, not an alternative to it

Hugo de Vries

a Dutch botanist and one of the first geneticists; developed the original mutation theory

mutation theory

developed by de Vries; new species evolve rapidly through sudden, large, and discontinuous genetic changes rather than slow, gradual variations

Ronald Fisher; John Burdon Sanderson Haldane; Sewall Wright

the three population geneticists who showed mathematically that Mendelian inheritance and natural selection working on small differences produce evolutionary change

Theodosius Dobzhansky; Ernst Mayr; George Gaylord Simpson; George Ledyard Stebbins Jr.; Bernhard Rensch

the five scientists who supported the modern synthesis, which combined Darwinism with Mendelian genetics

Motoo Kimura

a Japanese biologist best known for introducing the neutral theory of molecular evolution in 1968

the neutral theory of molecular evolution

much molecular change reflects genetic drift of variants with little or no effect on fitness, challenging the view that nearly every difference is adaptive

evolutionary developmental biology (evo-devo)

observes how changes in developmental genes and processes produce evolutionary changes in form

evolutionary genomics

comparison of whole genomes to study variation, phylogeny, and the genetic basis of adaptation

William Paley

an English clergyman who developed the argument from design/the watchmaker analogy

argument from design (watchmaker analogy)

complex, functional structures (like a watch or an eye) imply a designer (the Creator)

teleology

explaining something by the goal it serves; future benefits cannot cause present events; often used only as shorthand for a DNA-coded program shaped by past selection

Pax6/eyeless

the mouse Pax6 gene, when expressed in fruit-fly tissues, triggers development of fly eyes

tip (terminal axon)

a species or group at the end of a branch (living, or a sampled lineage)

branch

a lineage through time

node

a branch point representing a speciation event and the most recent common ancestor (MRCA) of everything beyond it

root

the base of the tree; the MRCA of all taxa shown

sister taxa/groups

two lineages that share a MRCA not shared with any other lineage

clade

an ancestor and all of its descendants (a monophyletic group)

outgroup

diverged before the ingroup’s common ancestor and is used to root the tree and polarize characters; provides the ancestral condition of characters for the ingroup, allowing states to be classified as ancestral or derived; assumes its lineage has changed relatively little since it split from the ingroup; not the ancestor of the ingroup and not necessarily

polytomy

a node with more than two descendant branches; usually indicates uncertainty (insufficient data), or very rapid successive speciation, not proof that several species arose at once

relationship

recency of common ancestry; the order of branching

monophyletic (clade) group

a common ancestor and all its descendants; the only kind that reflects a single evolutionary lineage; ex. mammals; birds; birds + crocodilians

paraphyletic group

a common ancestor and some but not all of its descendants (a subgroup is left out); traditional reptiles (excluding birds); fish (excluding tetrapods)

polyphyletic group

a group whose members descend from different ancestors; the group’s MRCA is not a member and lacks the shared trait, which evolved independently; warm-blooded animals (birds + mammals); flying vertebrates (birds + bats)

homology

similarity due to inheritance from a common ancestor, with or without change of function (mammalian middle-ear bones are homologous to reptilian jaw bones; forelimb bones of bats, whales, and humans)

analogy/homoplasy

similarity not due to common ancestry

convergence; parallel evolution; reversal

three kinds of homoplasy

convergence

independent evolution of similar traits in different lineages, such as wings of birds and insects, or streamlined bodies in sharks and dolphins

parallel evolution

occurs when independent, closely related species acquire similar traits or characteristics while adapting to similar environmental pressures

reversal

return to an ancestral state

plesiomorphy

an ancestral character state

apomorphy

a derived (evolutionarily novel) character state

synapomorphy

a shared derived state; the evidence that identifies monophyletic groups

symplesiomorphy

a shared ancestral state; uniformative for grouping

autapomorphy

a derived state unique to one lineage; uniformative for grouping because it arose after that lineage diverged

Willi Hennig

a German biologist and zoologist who is considered the founder of phylogenetic systematics, otherwise known as cladistics

Hennig’s principle (phylogenetic systematics/cladistics)

groupings must rest on shared derived characters, not on overall similarity or on shared ancestral traits

parsimony concept

chooses the tree (or reconstruction) that requires the fewest evolutionary changes; assumes that character changes are relatively rare, so hypotheses requiring fewer independent changes are more probably; does not assume homoplasy never occurs, and does not claim that evolution always follows the shortest path; a criterion for choosing the most plausible hypothesis

parsimony

character-based; counts changes on candidate trees; selects the tree with the fewest changes; changes are rare; can be misled when homoplasy is common or rates are very unequal

distance: UPGMA

pairwise distances converted to a tree by cluttering; produces a rooted tree; assumes equal rates on all lineages (molecular clock)

distance: neighbor-joining

pairwise distances; produces an unrooted tree; fast; does not assume equal rates across lineages

maximum likelihood

statistical; evaluates the probability of the observed data given a tree, branch lengths, and a model of sequence change; uses every site; can allow unequal substitution rates among bases and lineages; the tree with the highest likelihood is preferred; depends on the model; not the probability of the tree is correct; computationally intensive

Dollo’s law of irreversibility

an organism never returns exactly to a former evolutionary state, even under identical environmental conditions

Louis Dollo

a Belgian palaeontologist, known for his work on dinosaurs; he also posited that evolution is not reversible

gene tree

shows the history of copies of a gene

species tree

shows the history of the species

orthologs

homologous genes that diverged through speciation (the same gene in different species); normally more closely related in another species than a paralog in the same genome

speciation

the same gene in different species

paralogs

homologous genes that diverged through gene duplication (copies within a lineage)

gene duplication

copies within a lineage; usually precedes the speciation event in a two-gene family

horizontal gene transfer (HGT)

non-reproductive movement of genes between distantly related organisms; for example, carotenoid-synthesis genes moved from a fungus into aphids; a gene tree for such a gene will place the animal beside fungi even though the species tree does not

hybridization; hybrid speciation

two species interbreed and give rise to a new species; reproductive, unlike HGT

endosymbiosis

eukaryotes arose from a symbiosis between an archaeal host and a bacterium that became the mitochondrion, so the eukaryotic cell contains genomes with different ancestries

adaptive radiation

long-term evolution; many lineages diversifying in different directions

mosaic evolution

means different characters within a lineage evolve at different rates and times

molecular clock

a method used in evolutionary biology to estimate how long ago different species split (diverged) from a shared ancestor; does not automatically output years—it only counts genetic differences; assumes mutation rates remain roughly constant across different lineages

primates

change more slowly than many other mammals