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Biogeography Exam 3
| Question | Answer |
|---|---|
| systematics | describing/classifying species and uncovering evolutionary relationships |
| understanding evolutionary relationships | helps identify vulnerabilities, improve treatment strategies |
| conservation | depends on species identification |
| limited populations/ethics | make studying endangered species hard |
| surrogate species | provide insight without harming endangered species |
| taxonomy | naming/classifying organisms based on phylogenetic relationships |
| taxon | group of organisms assigned to classification category; should be monophyletic, common ancestor and all descendants |
| phylogeny | evolutionary history/relationships among species |
| phylogenetic trees | use shared traits to infer relationships |
| evolutionary systematics | convey relationships and traits; group organisms by shared traits; could result in paraphyletic groups |
| modern systematics | focus on shared ancestry and monophyletic groups |
| data chauvinism | no single data type is superior |
| problems with evolutionary systematics | early ideas lacked transparency/repeatability, subjective/non-testable hypotheses |
| phenetics | response to evolutionary systematics; uses clustering algorithms to group organisms; produces phenograms |
| phenograms | show distance between taxa based on traits |
| phenetics limitations | doesn’t accurately reflect relationships; sensitive to rates of evolution |
| phylogenetics | preferred for reconstructing evolutionary relationships |
| monophyly | important for recognition of taxa |
| phylogenetic systematics | uses objective methods, repeatable analyses, algorithm that replicates how evolution works to reconstruct evolutionary relationships |
| taxa examples | genus, species |
| taxa | can exist without reference to Linnaean hierarchy |
| descriptive works | describes/revises taxonomy of group of species and characteristics |
| systematic collections | specimen with locality info available for examination |
| binomen | genus and species in Latin |
| Latin | universal communication about species |
| codes of nomenclature | standardize endings/rules for changing names |
| name change reason | new data becomes available that affects hypotheses |
| type | name bearer, provides clarity in changes |
| holotype | single specimen that binomen is assigned to |
| neotype | single specimen replaces damaged/lost holotype |
| syntypes | specimens that represent species |
| lectotypes | syntype that serves as holotype |
| topotypes | specimens from type locality |
| paratypes | good candidates for neotype |
| type locality | location from which holotype came |
| new species | should have diagnosis that helps differentiate |
| geographic range | boundary of where species is found |
| phylogenetic taxonomy | based on relationships and sequencing data |
| phenetics taxonomy | based on observable traits |
| synonymy | when two species are found to be the same, older name is kept and newer is junior synonym |
| homonymy | same name for different species |
| diagnosis | key traits distinguish species |
| character | variable trait/feature |
| character states | specific forms of character |
| coding for phylogenetic analysis | identify variable character, code OTU, use morphological features as data |
| homologous characters | traits shared by 2+ taxa due to common ancestry; reflect evolutionary origin |
| homology criteria | position similarity, ontogenetic similarity, continuity across lineages |
| position similarity | topographic, geometric, placement |
| ontogenetic similarity | same embryonic cells |
| anagenesis | transformation of character state over time |
| cladogenesis | lineage splits into two distinct species |
| plesiomorphic | ancestral character state |
| apomorphic | derived character state |
| ingroup | group being studied |
| outgroup | closely related taxa to infer ancestral traits; determine character polarity; coded as 0 |
| derived character states | found only in ingroup; where trait evolved; coded as 1 |
| synapomorphy | shared derived character state; infers common ancestry |
| symplesiomorphy | shared ancestral character state |
| monophyletic group | comes from all descendants inheriting a trait |
| trait evolution | begins with mutation in single common ancestor |
| homoplasy | similar traits evolved independently in unrelated lineages |
| homology | traits inherited from common ancestor |
| saturation | DNA positions mutate repeatedly over time |
| species trees | represent overall relationships |
| phylogenetic trees | hypotheses |
| speciation | begins with common ancestor |
| sister species | share more recent common ancestor |
| nodes | speciation events |
| branches | species |
| OTUs | tips of branches |
| polytomies | unresolved branching in tree; reflects lack of data; resolved by adding derived character data |
| principle of parsimony | one origin is more likely than multiple; traits inherited from single mutation in common ancestor |
| character matrix | taxa vs. traits |
| reversal | trait evolves and is lost |
| different tree topologies | different hypotheses |
| consensus trees | collapse unsupported nodes into polytomies |
| strict consensus | only nodes present in all trees |
| majority rule consensus | nodes present in >50% of trees |
| heuristic searches | sample possible trees |
| character mapping | helps find simple explanations |
| phenograms | show genetic distance/branch length via phenetic algorithms |
| phylogenetic trees | show evolutionary relationships via characteristics |
| parsimony | tree with fewest evolutionary steps; simple |
| maximum likelihood | statistical models explain evolution; risk of circular reasoning |
| Bayesian likelihood | based on probability models; model-dependent |
| neighbor joining | distance-based |
| evaluating tree support | makes building trees transparent and scientific |
| consistency index | >1=fewer homoplasies; <1=more steps than characters |
| retention index | measure how well synapomorphies are retained |
| bootstrap support | resamples data; checks how often node appears |
| jackknife support | uses deletion instead of resampling |
| decay index | measures extra steps needed to collapse node |
| branch length | number of character changes on branch |
| Bayesian analysis | how likely node is to appear under given model |
| node is supported | high bootstrap, high decay index, high posterior probability |
| hierarchy | domain, kingdom, phylum, class, order, family, genus, species |
| genus | capitalized, italicized |
| species | lowercase, italicized |
| purpose of modern taxonomy | communicate evolutionary relationships and name only monophyletic groups |
| problem with traditional taxonomy | not all groups are monophyletic |
| taxonomic strategies | subordination and sequencing |
| subordination | name every node in tree with formal ranks |
| sequencing | name each branch as class without extra ranks |
| early biogeography | attempts to explain species distributions |
| species distributions | show why plants/animals live where they do |
| early attempts | guesses not based on measurable data |
| land bridges | used in early attempts to explain hypothetical connections between continents to show how species moved |
| dispersals | movement of species from one area to another |
| cladistic/vicariance biogeography | response to evolutionary systematics, testable hypotheses, objective methods |
| objective methods | repeatable algorithms |
| cladistic/vicariance biogeography methods | species treated as data points, species distribution infers about regions, parsimony algorithm |
| cladistic/vicariance biogeography critiques | early models ignored species dispersal |
| dispersal | overused, "lazy" explanation |
| cladistic/vicariance biogeography improvements | allows for speciation, penalizes extinction/dispersal |
| molecular analyses | help recover biogeographic histories, include phylogenetic analyses and DNA pattern distributions |
| biogeographic history | DNA helps reconstruct movements and speciation events |
| models | mathematical frameworks explaining distributions |
| molecular clocks | estimate when species diverged based on DNA mutation rates |
| Bayesian statistics | probability tests scenarios |
| problems with models/molecular clocks/Bayesian statistics | risk of circular reasoning, controversial methods |
Created by:
hlr2326