Final Flashcards
What is a central aim in biogeography?
Classify the world’s biota into meaningful geographical units for analysis
Endemism is…
To occur in one place and nowhere else (singular species)
Provincialism is…
Area of endemism, or, a coincident distribution of endemics in a particular place (multiple species)
Disjunction is…
The occurrence of close relatives in widely separated areas (think ratites)
What are the terms for the causes/patterns of endemism?
Autochthonous & Allochthonous
What does it mean to be autochthonous? Give examples
When a species is endemic to an area because it originated there and never moved
- Radiations following colonization of remote islands
- Isolation of biotas by vicariance
What does it mean to be allochthonous? Give examples
When a species is endemic to an area different from where it arose, due to the evolution of its range
- Pleistocene climate change caused species’ ranges to shift
- secular migration (shift in geographic range associated with evolutionary change; extinction in the area of origin)
What are the terms for old vs young endemics?
Paleoendemic (old)
Neoendemic (young)
What is the pattern of endemism?
nonrandom! Species ranges tend to be aggregated into biogeographic regions
Why are endemism patterns nonrandom?
Turnover within regions is relatively low & between regions, turnover is relatively high!
Species within regions may also tend to be more closely related; esp at larger spatial scales (this is due to time for speciation + dispersal = in situ origins)
What are key questions about biotic regions we should be asking?
- what criteria should be used to distinguish them?
- How many should be recognized?
- How do transition zones relate to geo history, geo features, and climate?
- How does recognizing regions help us conserve biodiversity?
Criteria for delimiting regions
Functional: Vegetation type (physiognomy)
Compositional (turnover in species occurrences - a taxonomic criterion)
What is functional classification of bio regions?
Classification of terrestrial biomes based on vegetation type due to its tight relationship with climate (temp and precip + soil conditions)
These biomes are NOT unique geographic regions; the same biome can occur in multiple places (Buffon’s Law -> different species in same biomes, due to convergent adaptations)
Sclater vs Wallace COMPOSITIONAL Criteria
Compositional = taxa-based, so biome doesn’t occur in multiple places (Nearctic, Neotropical, Oriental, etc)
Sclater: 6 terrestrial regions based on bird distribution
Wallace: 6 terrestrial regions based on non-volant mammals
What are compositional criteria? What are some interesting pattern examples?
Primary divisions following continental margins and major climatic patterns - taxon-based
Wallace’s & Lydekker’s Line -> Sunda and Sahul shelves
Explain geo history of Wallace’s and Lydekker’s Lines
Pleistocene: lowered sea levels exposed land connections between islands of each shelf, but the shelves themselves separated by deep water
Wallace’s line is north side of Wallacea, Lydekker is S side of Wallacea
Wallacea
Wallacea is seasonally dry monsoon climate (the area between Sahul and Sunda plates -> Australia and SE Asia)
Biota is characterized by high vertebrate endemism (40-60%)
Plant distributions less fidelity to the line
Explain how Sulawesi came to be
Largest island in Wallacea -> formed from convergence of 3 continental platese (Eurasian Sunda shelf), (Australasian Sahul shelf), and Pacific
How many biotic regions should be recognized? Compositional-based, ofc
SCALE DEPENDENT: inherently hierarchical..but is this real or an artificial assumption imposed by our models?
Non-hierarchical model: Grade of Membership
motifs
What are ecoregions?
Biotic regions delineated using both functional/compositional criteria for a specific purpose (like conservation)
- identify units for conservation action
What are biodiversity hotspots?
regions identified where exceptional concentrations of endemic species undergoing exceptional loss of habitat are
Endemism + functional criteria (region of elevated threat to habitat degradation)
Does Wallace’s Line represent a functional or compositional separation of biotic regions?
Compositional; turnover of taxa
How do we know if a temperate group has tropical origins?
Fossil record (but what about lack of fossil record?)
- current geographic ranges + phylogenetic trees!
What is the way to infer the most probable ancestral area state?
Maximum Likelihood -> what set of ancestral states maximized the probability of the states at the tips if changes are constant rate?
Parsimony doesnt consider branch lengths -> if rate of change is low, then ML matches parsimony
Geographic range is what type of property of a species?
Emergent
Modes of range evolution
Dispersal (expansion)
Local Extinction (range contraction)
Speciation
Explain Dispersal pattern with blob-o-gram
- Ancestral state (blob in one side)
- Dispersal (blob one side -> other side)
- Derived state (blob on both sides)
Explain Local Extinction pattern with blob-o-gram
- Ancestral state (blob on both sides)
- Local extinction
- Derived state (blob on only one side)
How many steps for a blobl to go from one side to the other side?
2 steps.
START: 1 side
- STEP to dispersal to other side
- STEP to extinction on ancestral side
END: 1 on other side
Explain speciation with blob-o-gram (node) (“SYMPATRIC”)
START: species in one area
- STEP of splitting in the one area
END: two species in the same area
- The ancestral range is SUBDIVIDED but doesnt mean ecologically sympatric!!!!!!) can still be allopatric in region!
Explain speciation with blob-o-gram (node) (“VICARIANCE”)
START: one species in both regions
- STEP the one species is isolated between the two regions
END: now two species, one in each region
The ranges of the descendants do NOT match the ancestral
Explain speciation with blob-o-gram (node) (“PERIPHERAL-ISOLATE”)
START: one species in both regions
- STEP: budding in one region
END: one species with same distribution as ancestral area, one species with just range in the budded region
What is a speciation scenario that cannot happen in the blob-o-grams?
Ancestor AB may. NOT give rise to descendants AB & AB (you cant have ancestral area being both, then splitting in both regions at the same time, then both descendants having the same distribution)
Dispersal-extinction-cladogenesis Model (DEC)
Range evolves by 2 modes:
- Anagenetic: dispersal & local extinction along branches
- Cladogenetic: subdivision and inheritance of ancestral range
In parsimony perspective, what events do not count in DEC?
Cladogenetic! only Anagenetic count (incur cost)
Larger ranges should have what affect on evolution of reproductive isolation?
Acceleration!
Ranges that span isolated regions should have what affect on evolution of reproductive isolation?
Acceleration! Reduced gene flow between isolated areas - like islands
What is jump dispersal?
Instant speciation by dispersal to an isolated area
What are the two ways area isolation accelerates speciation?
- Inhibition of gene flow
- isolated areas are more likely to have differences that promote local adaptation
What keeps biotas separate?
Barriers: transition zones between major regions (generally marked by physical features that inhibit dispersal - oceans, mountains, deserts)
Filters: permeable barriers via organisms adapted to withstand the crossing - no barrier is impermeable
Standstill Hypothesis
Human pops. diverged from Siberian ancestors 25kya -> beringia refugium during maximum; isolated until retreat 15-16kya for North American southward migration
buffon’s law & evolutionary convergence
Environmentally similar but isolated regions have taxonomically distinct biotas
Species may have similar ecological traits that have convergently evolves (think sclerophylls in Mediterranean climates)
Explain the GABI broadly
Great American Biotic Interchange
S America isolated during Cenozoic from other continents (“splendid isolation”)
- endemic mammal fauna evolved (think monkeys rafting, sloths, capybara, monotremes etc)
Isthmus of Panama closes = land bridge (3-4Myr, versus new model - 15Myr)
Explain GABI new “old isthmus” model
ancient river deposits of zircons = only come from Panama = 13-15myr
Explain GABI asymmetry
The net movement across isthmus is asymmetric, favoring a north to south colonization and diversification pattern (10% of north American species descend from S American immigrants versus 50% of S American species descend from N American immigrants)
What explains this asymmetry in the GABI (specifically nonvolant mammals)
- Northern lineages superior migrators; pre-adapted for savanna habitats that dominate the isthmus in the Pleistocene
- Northern lineages superior competitors; evolved on larger and more diverse continent = more “battle tested”
What is disjunction? Compare to Buffon’s Law
occurrence of closely related taxa in widely separated areas
Buffon’s Law: geographically isolated but environmentally similar regions harbor distinct communities of species
What were the two competing beliefs of range dynamics in the 19th century?
Catastrophism and Uniformitarianism (gradualism)
Explain catastrophism
- periods of stasis punctuated by cataclysmic change (extinction & creation)
- Georges Curvier
- Species do not change
- species ranges remain near site of creation
Explain uniformitarianism
- geological processes are slow but continual (mountain building for example)
- earth is ancient
- Charles Lyell
- species ranges can change
How did uniformitarians explain species ranges across continents when at the time, it was thought that the position of the continents were fixed?
Extensionists -> (Hooker, Lyell) dispersal across ancient land bridges
Dispersalists -> (Darwin, Wallace) long-distance dispersal; eventually won over
What were the two paradigmatic shifts of the 1970s?
- plate tectonics (sequential fragmentation and separation of continents)
- phylogenetic systematics (sequential branching of lineages)
Synapomorphies
shared derived characters
What are taxon-area cladograms?
branching history of species; substitute tips for areas
What is Hennig’s Progression Rule?
Progressively derived lineages move away from the ancestral area (Think Elepaio)
What is vicariance?
General patterns of disjunction caused by sequential emergence of barriers (phylogenies reveal vicariance history of the areas)
What pattern does long-distance dispersal show?
None! it is idiosyncratic and lineage-specific - it holds no predictive power for explaining general patterns
How might we falsify thee vicariance hypothesis?
The timing of divergence and timing of continental fragmentation do not align
Fossil taxon outside area of current occurrence
If many other clades do not show same pattern
What is the general area cladogram and who inspired it?
GAC = hypothesis of area history intended to be a common cause/explanation of disjunct distributions across unrelated taxa (inspired by Nelson and Platnick); so a lot of taxon-area cladograms together
What are inconsistent patterns with vicariance?
- Failure to speciate
- Redundant distributions (multiple endemic lineages to same region)
- Missing distributions
Three processes that lead to disjunction
- Vicariance
- Extinction
- Dispersal
What does true congruence require?
Matching of topology of branching and the times of divergence
Kinds of islands
- oceanic (volcanic)
- continental shelf
- continental fragment
- habitat
What is the species-area relationship?
of individuals per species is lognormally distributed (few species are common, many are rare); richness increases with area sampled
Linear log-log function for species-area relationship; explain terms
log(S) = log(c) + zlog(A)
S: species #
A: area sampled
z: how quickly number of species increases (slope)
log(c): expected # of species in 1 unit of area
Island Species-Area relationship
Larger islands = more species
How do values of z (slope) in the species-area equation change for islands vs mainland?
Islands: higher
Nested samples of mainland: lower
Species-isolation relationship
of species declines with island isolation (exponentially or sigmoidally); isolation is measured in distance, barrier permeability, time, etc.
Why do smaller islands have fewer species than equal-sized area of mainland?
Smaller populations are more prone to extinction
Why do more-isolated islands have fewer species than less-isolated ones?
Less likely to be colonized by immigrants
MacArthur and Wilson Equilibrium model of island biogeography
of species on an island is the net result of opposing processes (immigration and extinction)
Explain S, P, I, and E in the island Equilibrium Model
S = # of speciees on an island (Immigration & Extinction = net)
P = theoretical maximum # of species available for immigration from mainland
I = immigration rate (declines as S approaches P)
E = extinction rate (increases as S approaches P)
What type of equilibrium is the Equilibrium Model of Island Biogeo
dynamic and stable (new species arrive & others die; returns to equilibrium if disturbed)
Explain island size and extinction relationship
smaller island = higher rates (size constrains population) & also, extinction due to stochastic fluctuations in birth and death
Explain isolation and size for rates of immigration and extinction on islands; including equilibrium turnover and species number
Near island: higher rates immigration
Small island: higher rates extinction
Small Near Island: highest equilibrium rate of turnover
Large Far Island: lowest equilibrium rate of turnover
Largest S (# of species): large near islands
What is the target area effect?
immigration rates should be higher on larger islands than smaller islands
What is the rescue effect?
extinction rates should be lower on near islands due to conspecific immigration (gene flow) from mainland populations
Does M&Ws equilibrium model consider evolution?
No! It is only ecological. It does not consider in situ speciation & endemism
What is ecological release?
Colonization of a place devoid of pressures from competition/predation = allow shift/expansion in niche (pronounced on small remote islands)
What is adaptive radiation?
single colonizing lineage diversifies into separate species with more specialized nichees
List some Hawaiian radiations
Silverswords
Honeycreepers
Bidens (haha)
What do the biotas of islands neither near nor far from a continental biota reflect?
Dynamics of:
- colonization from mainland
- colonization between islands
- adaptation and speciation within and between islands
What are taxon cycles?
Colonization, adaptation, speciation, and extinction on archipelagos have distinct phases
What is the evidence for taxon cycles?
Range size (endemism) and ecological differentiation
1. Initial expansion
2. Differentiation, specialization, speciation
3. Contraction
4. Relictual endemism
What is the island rule of body size evolution in mammals?
Pervasive, but not universal, trend that on islands, small mammal species become larger (gigantism) and large species become smaller (dwarfism)
Also in birds, reptiles - but not amphibians
Why does the island rule of body size in mammals happen?
Small species: ecological release from competition and predation = larger species niches open
Large species: ecological release from competitors in smaller niches & resource-limited = favor smaller size
What is flightlessness driven by?
limited resources, ecological release from predators (reduction of metabolically expensive flight; gigantism)
What are evolutionary consequences of flightlessness and reduced dispersal ability?
- traits aiding in colonization now maladaptive (disperse past island bounds = nowhere to go; die)
- reduced gene flow among islands and between populations = accelerate speciation
What is Baker’s Law?
Self-fertilizing plants are more likely to colonize islands because only 1 individual is needed
What is dioecy?
separation of sexes (often an outcrossing mechanism); sometimes comes after island colonization to replace self-incompatibility
What scale are phylogeographic studies?
Shallower; focus on geographic patterns and processes
What are some examples of questions you can ask in the study of phylogeography?
- origination point
- spatial genetic structure (how are populations bounded)
- migration -> how/when and where has gene flow occurred?
- historical demographics & spatial patterns
- comparative phylogeographic historiees
What was an early assumption about gene trees?
That they accurately represent phylogeny, but coalescence is stochastic…
What is incomplete lineage sorting?
the stochastic coalescent event that does not follow true species relationships
What is the probability of coalescence?
1/(2N)
N diploid individuals in each generation, two random alleles coalesce in generation previous
What is the expected time to coalescence?
2N generations; geometric distribution, but coalescence is highly variable
What is the multi-species coalescent model?
It provides the likelihood of a gene tree topology given a branching history of populations through time (takes into account topology, branch lengths (time), and branch widths (population size))
What is the ideal gene for phylogeographic analysis?
One that coalesces rapidly and has a high rate of mutation (fast evolving genes!)
What makes organellar genomes good for phylogeographic study? What makes them bad?
They are uniparentally inherited (haploid), meaning that their expected time to coalescence is ONE QUARTER that of autosomal nuclear genes - but it lacks recombination, so it acts as a single gene!
What are common methods of NGS?
target enrichment (gene trees)
RADseq (SNPs)
WG resequencing (mapped to reference)
Linked vs unlinked SNPs
linked SNPs: build gene trees (linked gene by gene)
unlinked: just SNPs in general; can still enable inference of population tree
What models are best for shallow population histories?
Drift-based (unlinked SNPs & allele frequencies -> no mutation, just neutral drift)
Explain D statistics / ABBA BABA test
Infer gene flow using 3 tips and an outgroup
ABBA = gene flow between inner branches
Explain ABBA BABA frequencies and conclusions from them
Equal ABBA BABA = ILS
ABBA»_space; BABA = gene flow between 1 and 2
(3, 2, 1, O)
List the mass extinctions
Ordovician (445 Mya)
Late Devonian (370 Mya)
Permian-Triassic (252 Mya)
Triassic-Jurassic (201 Mya)
Cretaceous-Paleogene (65 Mya)
Anthropocene (current)
What percent do anthropogenic biomes cover Earth’s ice-free land survace?
75%
What are the evidences for the Anthropocene being a distinct epoch?
Technofossils (concrete, plastic, aluminum)
Fossil fuel combustion (black carbon)
Deforestation & road construction (erosion)
Geochemical signatures (pesticides)
Atmospheric carbon dioxide & methane
Global Temps & sea levels
How have humans affected the distributions of species?
Extinction of native species
Spread of non-native species
Climate change-induced range shifts
New and altered selection pressures and niches
What is the trend of island vs mainland extinctions caused by humans?
Mainland increased in 20th century
What have we done that causes extinction?
Introduction of alien species, habitat loss
What are extinctions preceded by?
Range contraction and subsequent collapse
What are the melting range and contagion hypotheses?
Melting Range: extinctions proceed from edges towards core
Contagion: extirpation proceeds towards periphery (more common in observed range collapses - like taxon cycles)
What is the Linnean shortfall?
incomplete knowledge of the total number of species out there, so rates of extinction are extrapolations
What are some vectors of exotic species?
Agriculture
Transport
Pest control
Corridor creation (panama canal)
What is the elevator effect?
Mountains and high-latitude regions are sensitive to change and experience highest rates of global warning. Species ranges shift upwards in response to warming, effectively causing species at the top to be driven to extinction because it is too warm
What are some examples of how species have adapted/reacted to urban environments?
- higher mutation rates
- chemical defenses
- decreased genetic diversity
What are the reasons that we think biotic regions are hierarchical?
- a range of a taxon is nested within the ranges of its higher taxa (species, genus, family)
- strongest ecological forces shape the largest regional divisions and are weaker at smaller spatial scales
- hierarchical sequence of continental fragmentation of Pangea
What are biogeographically meaningful units?
organization that reflects responses to abiotic and biotic forces -> shared evolutionary history of lineages, shared tectonic history of areas
What are the parameters controlling interchange (GABI)?
Dispersal Rates
Speciation & extinction rates of colonizing clades
(N clades migrators = >D; N clades competitors = >S or <E)
Who were Nelson and Platnick?
Two guys who adapted vicariance hypothesis -> phylogenies are valuable to biogeography; reveal patterns of disjunction caused by vicariance
Plant vs Animal patterns of vicariance with gondwana
animals = congruence
Plants = dispersal more frequent, discordant directions
What is the pattern of phylogenesis (in situ speciation; evolution) on islands regarding size and distance?
Speciation to endemic species richness increases with isolation (time and distance)
What is pseudo-congruence?
Matching topologies but not times
What is the loss of dispersal ability in plants associated with?
- island colonization
- shifts from marginal disturbed habitats to stable interior forests (heavier seeds); taxon cycle
What are the challenges of inferring population trees for phylogeography?
closely related & recently diverged lineages = short wide branches (so high discordance)
Mutation required to estimate gene tress - dont have much time to accumulate
