3First…what is a species? Biological species conceptpopulation whose members can interbreed & produce viable, fertile offspringreproductively compatibleDistinct species: songs & behaviors are different enough to prevent interbreedingHumans re so diverse but considered one species, whereas these Meadowlarks look so similar but are considered different species.Meadowlarks Similar body & colorations, but are distinct biological species because their songs & other behaviors are different enough to prevent interbreedingEastern MeadowlarkWestern Meadowlark3
4But that doesn’t capture every situation Consider Ensatina salamanders. How many species? Which ones are different species?
5Species Definitions Other definitions include: Morphological or typological - They conform to the same body plan.Phylogenetic or evolutionary - Share a common ancestor and a unique evolutionary history.Ecological - Share a specific niche, unique to them and them alone.“Species” is a human language box. Never forget that nature exists on a continuum!
6DiscussionWhich definitions work or don’t work to determine whether or not you’re examining different species if you’re studying…Bacteria in a lab petri dish?Hooved mammals in the modern-day arctic?Dinosaurs?Ancient algae?
7How and why do new species originate? Species are created by a series of evolutionary processespopulations become isolated - no gene flow between themgeographically isolated and/orreproductively isolatedisolated populations evolve independentlyIsolationallopatricgeographic separationsympatricstill live in same area7
8PRE-zygotic barriers An obstacle to mating or fertilization geographic isolationecological isolationtemporal isolationbehavioral isolationmechanical isolationgametic isolation8
9Geographic isolation Species occur in different areas physical barrier Ammospermophilus sppGeographic isolationSpecies occur in different areasphysical barrierallopatric speciation“other country”Harris’s antelope squirrel inhabits the canyon’s south rim (L). Just a few miles away on the north rim (R) lives the closely related white-tailed antelope squirrel9
10Ecological isolationSpecies occur in same region, but occupy different habitats so rarely encounter each otherreproductively isolated2 species of garter snake, Thamnophis, occur in same area, but one lives in water & other is terrestriallions & tigers could hybridize, but they live in different habitats:lions in grasslandstigers in rainforest10
11Temporal isolationSpecies that breed during different times of day, different seasons, or different years cannot mix gametesreproductive isolationsympatric speciation“same country”Eastern spotted skunk (L) & western spotted skunk (R) overlap in range but eastern mates in late winter & western mates in late summer11
12Behavioral isolation sympatric speciation? Unique behavioral patterns & rituals isolate speciesidentifies members of speciesattract mates of same species courtship rituals, mating callsreproductive isolationThe most comedic species of the Galapagos Islands is the Blue Footed Booby, what a ridiculous outfit and expression! Their name is in fact taken from the Spanish 'bobo' which means clown.The Blue Footed Boobies above display part of their humorous courtship ritual whereby they raise their feet one at a time and then swivel their heads away from the prospective mate looking to the sky.Other interesting Booby features are the highly evolved airbag systems in their skulls which allow them to dive bomb into the sea for fish from great height, and the egg and hatchling nesting boundaries they make which are rings of Boobie poop. They aren't the only Booby on the island — there are also Masked and Red Footed Boobies about.Blue footed boobies mate only after a courtship display unique to their species12
13Recognizing your own species courtship songs of sympatric species of lacewingscourtship display of Gray-Crowned Cranes, Kenyafirefly courtship displays13
14Mechanical isolation Plants sympatric speciation? Morphological differences can prevent successful matingreproductive isolationPlantsEven in closely related species of plants, the flowers often have distinct appearances that attract different pollinators. These 2 species of monkey flower differ greatly in shape & color, therefore cross-pollination does not happen.The most comedic species of the Galapagos Islands is the Blue Footed Booby, what a ridiculous outfit and expression! Their name is in fact taken from the Spanish 'bobo' which means clown.The Blue Footed Boobies above display part of their humorous courtship ritual whereby they raise their feet one at a time and then swivel their heads away from the prospective mate looking to the sky.Other interesting Booby features are the highly evolved airbag systems in their skulls which allow them to dive bomb into the sea for fish from great height, and the egg and hatchling nesting boundaries they make which are rings of Boobie poop. They aren't the only Booby on the island — there are also Masked and Red Footed Boobies about.14
15Mechanical isolation Animals For many insects, male & female sex organs of closely related species do not fit together, preventing sperm transferlack of “fit” between sexual organs: hard to imagine for us… but a big issue for insects with different shaped genitals!The selection is intense because it directly affects offspring production -- it is affecting sex itselfDamsel fly penises15
16Gametic isolation sympatric speciation? Sperm of one species may not be able to fertilize eggs of another speciesmechanismsbiochemical barrier so sperm cannot penetrate eggreceptor recognition: lock & key between egg & spermchemical incompatibilitysperm cannot survive in female reproductive tractSea urchins release sperm & eggs into surrounding waters where they fuse & form zygotes. Gametes of different species— red & purple —are unable to fuse.16
17POST-zygotic barriers Prevent hybrid offspring from developing into a viable, fertile adultreduced hybrid viabilityreduced hybrid fertilityhybrid breakdownzebroid17
18Reduced hybrid viability sympatric speciation?Reduced hybrid viabilityGenes of different parent species may interact & impair the hybrid’s developmentSpecies of salamander genus, Ensatina, may interbreed, but most hybrids do not complete development & those that do are frail.18
19Reduced hybrid fertility Even if hybrids are vigorous they may be sterilechromosomes of parents may differ in number or structure & meiosis in hybrids may fail to produce normal gametesMules are vigorous, but sterileWhat’s wrong with having 63 chromosomes?Odd number! Cannot pair up in meiosis.Horses have 64 chromosomes(32 pairs)Donkeys have 62 chromosomes(31 pairs)Mules have 63 chromosomes!19
20sympatric speciation?Hybrid breakdownHybrids may be fertile & viable in first generation, but when they mate offspring are feeble or sterileIn strains of cultivated rice, hybrids are vigorous but plants in next generation are small & sterile.On path to separate species.20
21Rate of SpeciationWhen considering speciation events over geological time: Does speciation happen gradually or rapidly, uniformly or unevenly?GradualismCharles DarwinCharles LyellPunctuated equilibriumStephen Jay GouldNiles EldredgeNiles EldredgeCuratorAmerican Museum of Natural History21
22Gradualism Gradual, constant divergence over long spans of time big changes occur as the accumulation of many small onesevents can increase or decrease speciations worldwide, but overall speciation proceeds fairly regularly22
23Punctuated Equilibrium Rate of speciation is not constantOrganisms are in “stasis” for much of their history, with little or no changeWhen speciation occurs, it tends to be in a rapid burstSpecies undergo rapid change when they 1st bud from parent populationTime23
24DiscussionBased upon what you know of evolutionary history, where do you fall: gradualism or punctuated equilibrium supporter?
25Speciation RatesRegardless of whether punctuated equilibrium or gradualism holds, speciation rates vary by species and circumstanceSpeciation can occur over a scale of millions of years, or much more rapidly!Polyploidy in plants increases speciation rate to, in some cases, only a few years
26Polyploidy and Hybrid Speciation Unlike in animals, in plants, duplicating the genome (polyploidy) isn’t fatal.Plants hybridize more often and more readily than animals on averageSometimes in plants, a diploid hybrid is sterile, but a triploid or tetraploid hybrid isn’t due to the mechanisms of chromosome alignment in their haploid life phase.
27Polyploidy and Hybrid Speciation Polyploid offspring may reproduce with other polyploids, or re-reproduce with a parental type, or may self-fertilize (oh plants, you so crazy)But by any of the three mechanisms, polyploids wind up reproductively isolated from the parental population, but produce non-sterile offspring = they’re a new population that evolution will be acting upon! A new species, in as little as a generation!
28Polyploidy and Hybrid Speciation This has been observed in species like the Evening Primrose, Raphanobrassica, Hemp Nettle, and the Maidenhair Fern.
29Speciation RatesIn all species, when a new habitat or new niche becomes available, speciation rates tend to increaseAdaptive radiation - ecological & phenotypic diversity in a rapidly multiplying lineage
30DiscussionScientists generally break it down into two main reasons why this causes a burst in speciation events. What do you think they could be?
31Speciation Rates Ex: Darwin’s finches Ex: An explosion in bivalve species diversity after the loss of brachiopods in the “Great Dying,” or Permian extinction 250 mya
32Extinction But, of course, extinction rates also fluctuate Higher in times of environmental stress% of familiesextinctMillion years ago
33DiscussionA population’s ability to respond to environmental changes is dictated, in part, by its level of genetic diversity.Which do you think is most resistant to extinction and why: high-genetic-diversity or low-genetic-diversity?
34Morphological, Molecular, and Other Lines of EvidenceMorphological, Molecular, and Other
35Lines of EvidenceModes of investigation into evolutionary history includeMorphologicalMolecularDevelopmental (which is part Morphology, part Molecular Biology)Geographical*Geological*Active change* - Not addressed in notes - read up on basic definition of biogeography, fossil record at home
36Discussion What is the relationship between: …and WHY? Recency of two populations’ last common ancestorAmount of similarity between populationsDegree of relatedness between populations…and WHY?
37Morphological Evidence Morphology = body formShared deep body structures are evidence of shared ancestry, but appearances and functions aren’t necessarily… why not?
38Anatomical record Homologous structures similarities in characteristics resulting from common ancestry
39Homologous structures Similar structureSimilar developmentDifferent functionsEvidence of evolutionary relationship
41Homologous Structures Produced by divergent evolutionYour typical “population divided, evolves in two separate directions” scenarioStructure present in ancestor passed down to descendents
42Analogous structures Separate evolution of structures similar functionssimilar external formdifferent internal structure & developmentdifferent originno evolutionary relationshipSolving a similar problem with a similar solution
43Analogous Structures Flight evolved in 3 separate animal groups evolved similar “solution” to similar “problems”
44& sleek bodies are analogous structures! Fish: aquatic vertebratesDolphins: aquatic mammalssimilar adaptations to life in the seanot closely relatedThose fins & tails& sleek bodies are analogous structures!
45Analogous StructuresAnalogous structures produced by convergent evolution or parallel evolutionConvergent evolution: Two separate, asynchronous (different times, different ecospaces) evolutionary lineages develop a similar trait/solutionExample: pillbugs and pillmillipedes both develop similar defenses, but didn’t inherit them from a so-defended shared ancestor
46Parallel Evolution marsupial mammals placental mammals Like convergent evolution, but the two species evolve at the same time and/or in the same ecospacefilling similar ecological roles in similar environments, so similar adaptations were selectedmarsupialmammalsplacentalmammals
48Vestigial structuresModern structures that have reduced or no functionremnants of structures that were functional in ancestral speciesdeleterious mutations accumulate in genes for non-critical structures without reducing fitnesseyes on blind cave fishare a kind of homology
49Vestigial organs Hind leg bones on whale fossils and modern whales Why would whales have pelvis & leg bones if they were always sea creatures?
50Vestigial structuresSpurs or tiny leg bones in snakes
51Vestigial structuresArrector pili, post-caudal tail, appendix in humans
52Molecular Evidence Evidence from genes & proteins The most powerful and commonly-used these days, in part because the data set is so vast and in part because it’s easily quantifiable
53“Conservation”What does it mean to say a homologous sequence or structure is “highly conserved?”Means it’s extremely similar or identical amongst the organisms that inherited itConserved sequences = useful evidence in uncovering ancestry
54Conserved StructuresExample, metabolic pathways = highly conserved across all domains of life (archaea, bacteria, eukarya)A remnant of life’s common ancestryBacterial metabolic enzymes - notice, more of them are common to all 3 domains than are at all unique
55Conserved StructuresExample: Structural evidence supports the relatedness of all eukaryotesMore than just the nucleus is conserved… linear chromosomes, membrane-bound organelles, and endomembrane systems are as well
56Molecular recordMolecular evidence elegantly demonstrates the relatedness of all lifeuniversal genetic code! The ultimate “conserved sequence” - the whole darned thing!DNA, RNA, proteins - genome, transcriptome, proteomeClosely related species have sequences that are more similar than distantly related speciesDNA & proteins are a molecular record of evolutionary relationships
57Discussion“The more similar genetic loci two populations share, the more related they are”WHY would this be??
58Conserved SequencesThink of a conserved sequence (which can be as little as a single base pair) as being a genetic homologous structure
59Conserved Sequences Suppose an ancestral population has the sequence AAGTCTTTAGCTAGCTGGCTGTat a particular locus.Over time, it accumulates mutations. Demo!
60P F1 F2 F3 AAGTCTTTAGCTAGCTGGCTGT AAGTCTTTATCTAGCTGGCTGTAAATCTTTAGCTAGCTGGCTGTAGGTCTTTATCTAGCTGGCTGTF2AAATCTTTAGCTAGCTGTCTGTAAGTCTTTATCTAGCTGGCTGGAAATATTTAGCTAGCTGGCTGTAAATCCTTAGCTAGCTGTCTGTCAGTCTTTATCTAGCTGGCTGGAAGTCTTTATCTAGCTGGGTGGAAATCTCTAGCTAGCTGTCTGTF3AAATATTTCGCTAGCTGGCTGTAAATATTTAGCCAGCTGGCTGTWhat % of DNA do these two share?Are they closely related?What % of DNA do these two share?Are they closely related?Can you spot any conserved sequences among the modern (F3) species?
61DiscussionSuppose you have this information for locus ß135 in three similar species.Species A: AGCTTCGATTGCTAGCTASpecies B: AGCTACGATTGGTAGCTASpecies C: AGCTACGACCTTGGTAGCTAWho’s most related? Who shares the most recent LCA?
62It works for proteins, too! HumanMacaqueDogBirdFrogLampreyWhy does comparing amino acid sequence measure evolutionary relationships?8324567125102030405060708090100110120Number of amino acid differences betweenhemoglobin (146 aa) of vertebrate species and that of humans
63Molecular EvidenceAn organism’s evolutionary history is documented in its genome!How many similarities are shared between populations?DNA hybridization experimentsTrack SNPs (single nucleotide polymorphisms), conserved sequences, common loci, duplicated genesAnalyze pseudogenes (“vestigial genes”)Even analyze whole genomes…
64Genome sequencingWhat can data from whole genome sequencing tell us about evolution of humans?
65Primate Common Ancestry Chromosome Number in the Great Apes (Hominidae)orangutan (Pogo) 48gorilla (Gorilla) 48chimpanzee (Pan) 48human (Homo) 46Could we have just lost a pair of chromosomes?Hypothesis: Change in chromosome number?If these organisms share a common ancestor, then is there evidence in the genome for this change in chromosome number
66Ancestral Chromosomes Chromosome Number in the Great Apes (Hominidae) Chromosomal fusionTestable prediction: If common ancestor had 48 chromosomes (24 pairs), then humans carry a fused chromosome (23 pairs).Ancestral ChromosomesFusionHomo sapiensChromosome Number in the Great Apes (Hominidae)orangutan (Pogo) 48gorilla (Gorilla) 48chimpanzee (Pan) 48human (Homo) 46Inactivated centromereTelomere sequencesCentromereTelomere
67Test of the Human Genome Hillier et al (2005) “Generation and Annotation of the DNA sequences of human chromosomes 2 and 4,” Nature 434: 724 – 731.Test of the Human GenomeAncestral Chromosomes“Chromosome 2 is unique to the human lineage of evolution, having emerged as a result of head-to-head fusion of two chromosomes that remained separate in other primates. The precise fusion site has been located in 2q13–2q14.1, where our analysis confirmed the presence of multiple subtelomeric duplications to chromosomes 1, 5, 8, 9, 10, 12, 19, 21 and 22. During the formation of human chromosome 2, one of the two centromeres became inactivated (2q21, which corresponds to the centromere from chimp chromosome 13) and the centromeric structure quickly deterioriated.”FusionHomo sapiensInactivated centromereTelomere sequencesChr 2Human Chromosome #2 shows the exact point at which this fusion took place
68DiscussionIf you want to analyze the evolutionary history of an order, a phylum, a kingdom, etc., what kinds of genes do you think would be most productive to study?
69Molecular Clocks Some genes show a constant rate of mutation/evolution They can be used as molecular clocks and used to calculate the time since divergence, calibrated against branches whose dates are known from the fossil record9060Number of mutations30306090Divergence time (millions of years)
70Molecular ClocksExample: Use of molecular clocks demonstrates that HIV leapt from simians to humans in the 1930s
710.200.15HIVIndex of base changes between HIV gene sequences0.10RangeAdjusted best-fit line(accounts for uncertaindates of HIV sequences)0.05190019201940196019802000Year
72Evo-Devo: Morpho+DNA Evidence Comparative embryology reveals anatomical similarity not visible in adultsEx: all vertebrate embryos have similar structures at similar stages of developmentgill pouch in fish, frog, snake, birds, human, etc.Pharyngeal pouchesPost-anal tailChick embryo (LM)Human embryo
73Evo-DevoMajor changes in body form can result from changes in the sequences and regulation of developmental genesGenes that program development control the rate, timing, and spatial pattern of changes in an organism’s form as it developsEx: A change in the rate of gene expression produces very different skulls from the same genesChimpanzee fetus -> adultHuman fetus -> adult
74Evo-DevoEx: A change in spatial expression of the Hox gene produces body parts in a new location, without a change in coding genesHox gene 8Hox gene 6Hox gene 7About 400 myaRepeated Hox expression extends bodyArtemiaDrosophila
75Evo-DevoAmong MANY other evolutionary applications, these means that modern organisms have many ancient genes still in place that can be used to study the ancestral formThose genes are just producing different phenotypes now because of changes to regulatory sequences
77“descendants” of wild mustard “descendants” of the wolf Artificial selectionArtificial breeding can use variations in populations to create vastly different “breeds” & “varieties”“descendants” of wild mustard“descendants” of the wolf
78Selective breedingthe raw genetic material (variation) is hidden there
79Selective breedingHidden variation can be exposed through selection!
83“Tree Thinking”Phylogeny is the evolutionary history of a species or group of related speciesSystematics uses fossil, molecular, and morphological data to infer evolutionary relationships and classify organismsDepict these relationships in branching cladograms or phylogenetic trees
84Order Family Genus Species Panthera pardus (leopard) Felidae Panthera Taxideataxus(Americanbadger)TaxideaCarnivoraMustelidaeLutra lutra(Europeanotter)LutraCanislatrans(coyote)CanidaeCanisCanislupus(gray wolf)84
85Phylogenetic TreesA phylogenetic tree is a hypothesis about evolutionary relationshipsMoves forward in time from the rootEach branch point represents a shared common ancestor (usually not labeled)Sister taxa represented by the tips of the branches
86where lineages diverge Taxon A Branch point:where lineages divergeTaxon ATaxon BSistertaxaTaxon CTaxon DTaxon EANCESTRALLINEAGETaxon FTaxon GThis branch pointrepresents thecommon ancestor oftaxa A–G.This branch point formsan unresolvedpattern of divergence, sharedby taxa D, E, and F.86
87Discussion – Who is most related? Where’s the LCA? Lizardsand snakesCrocodiliansOrnithischiandinosaursCommonancestor ofcrocodilians,dinosaurs,and birdsSaurischiandinosaursBirds87
88Phylogenetic Trees - Limitations & Rules Show patterns of descent, not phenotypic similarity. Don’t necessarily indicate how long ago species diverged, or how much it’s changed since then.Taxa DID NOT evolve from any sister taxa!
89CladisticsTrees are constructed based on homologies, physical or molecularCladistics groups organisms by common descent.A clade = a group of species that includes an ancestral species and its descendentsTo be valid, a clade must be monophyletic - include all descendent species, and no non-descendents
91Cladistics Invalid clades are Paraphyletic – Includes the ancestor but not all of its descendentsPolyphyletic - Includes some species that do not share the ancestor in question
92(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic groupAAABGroup BBGroup CCCDDDEEGroup EFFFGGG92
93Valid Clades Are reptiles monophyletic, paraphyletic, or polyphyletic? Should “reptile” be a valid classification?
94CladisticsWhen comparing it to its ancestor, a species/clade displays various homologies.Shared ancestral characters - originated in an ancestor, shared with all members.Shared derived characters - An inherited novelty unique to that clade.
95Cladistics Can use either morphological or molecular homologies Generally, a chart with + or 1 for “has it,” 0 or - for “doesn’t”To construct a tree, examine shared and derived characters, and follow the principle of parsimony, also called Occam’s Razor: the simplest explanation is usually the best.
96TAXA (outgroup) Lancelet Lamprey Leopard Bass Frog Turtle Vertebral Discussion – Practice!TAXA(outgroup)LanceletLampreyLeopardBassFrogTurtleVertebralcolumn(backbone)11111Hinged jaws1111Four walkinglegsCHARACTERS111Figure Constructing a phylogenetic tree.Amnion11Hair1(a) Character table96
97VariationsCladograms can be constructed to show time or distance since divergence, amount of difference…Trees can take different shapes: angled splits, square splits, circular…
98Branch lengths indicate time DrosophilaLanceletZebrafishFrogChickenHumanMousePALEOZOICMESOZOICCENOZOIC54225165.5PresentMillions of years ago98