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Phylogenetics
The science of figuring out relationships between organisms
Phylogeny
A hypothesis of evolutionary interrelationships of a group of species/populations, usually shown as a tree
Systematics
The science of classifying organisms based on their characteristics/relationships
Taxonomy
Part of systematics - concerned with naming organisms
Cladistics (Phylogenetic Systematics)
Classification of organisms based on their order of branching
Branch point
Where lineages diverge = speciation (or most recent common ancestor)
Sister taxa
Two taxa that share an immediate common ancestor and are each others closest relatives on the tree (google)
Basal Taxon
Taxon that branched off earlier than the others in the tree, but still inside the clade
Polytomy
a node on a phylogenetic tree that splits into more than two branches
Soft polytomy
an unresolved pattern of divergence - a polytomy due to lack of information.
Hard polytomy
A real three-way split (that actually happened in nature)
Linnaeus
18th century taxonomy (in many ways the founder of systematics)
Linnean System
- Includes binomial nomenclature and hierarchical classification system (e.g. kingdom, phylum, class, order, family, genus, species)
- Still in use today (although domain has been added as most inclusive hierarchical category)
- Today, the Linnean system is used assuming the named taxa show some sort of relationship (usually monophyletic)
Correct order of Linneaus’s heirarchical classification system
Domain, kingdom, phylum, class, order, family, genus, species
Do kids prefer candy over fresh green salad?
Microevolution
evolution within a species (for example colored moths)
Macroevolution
Speciation, extinctions, evolutionary trends (like becoming bipedal over time)
Nodes
Branching points that are speciation events
Monophyletic group (clade)
An ancestor and all of its descendants (cladistics emphasizes only monophyletic groups)
Paraphyletic group
A group that includes a common ancestor and some (but not all) of its descendants. (e.g. reptiles as they were originally defined was paraphyletic because it left out birds)
Polyphyletic group
A collection of organisms grouped together based on shared physical traits or habits, but do not share a common ancestor (e.g. warm-blooded animals)
Phylogenies can be inferred from...
morphological and molecular homologies. Homologies show developmental, structural, and genetic (similar expression of genes) similarities due to shared ancestry.
Convergent evolution can lead to...
analogous (homoplastic - similar in shape) traits:
- similar, analogous, trait that evolved independently in each lineage (homoplasy)
- brought on by natural selection due to similar environment rather than shared ancestry.
- e.g. most monkeys eat fruits but Howler monkeys and Colobus monkeys have independently evolved complex stomachs to handle a folivorous diet.
- e.g. body types of dolphins and sharks
Homoplasy (homoplastic or analagous characters)
Analogous (or convergent) characteristics
- e.g. Marsupial mole (from Australia) vs Golden mole (from Africa)
- Molecular homoplasy - identical or similar DNA, RNA, or amino acid sequences in different species that did not inherit the similarity from a common ancestor
Synapomorphies
Shared derived characters
- new characteristics relative to earlier forms
- most useful for figuring out relationships
- e.g. humans and gorillas having larger brains
Homologous characters
Physical or genetic features in different species that were inherited by a common ancestor (regardless of whether they have changed)
- ancestral characters
- synapomorphies
Plesiomorphies
Ancestral characters = characters that were inherited from ancestors
e.g. the vertebrae
How to distinguish relationships (given confusion around analogous vs homologous traits and plesiomorphies vs synapomorphies)
- Phylogenetic trees based on many traits and/or extensive molecular data (many genes)
- Relationships among living forms can be compared to fossil evidence (or vice versa) (ex. birds and mammals)
- Parsimony and Parametric (statistical) methods
What are the methods for finding the best cladograms?
Parsimony - pick the tree(s) with the fewest evolutionary steps
Parametric (statistical methods)
Parsimony
- Based on Occam's Razor - when you have two competing hypotheses that make the same predictions, the simpler hypothesis is more likely to be correct. (cut away unnecessary complex ideas and "ad hoc" assumptions)
- William of Ockham (14th Century)
- Parsiomy in phylogenetics - Pick the tree(s) with the fewest evolutionary steps.
William of Ockham (14th Century)
Created Occam's Razor - parsimony, in science
- Occam's Razor (parsimony in the science context) - when you have two competing hypotheses that make the same predictions, the simpler hypothesis is more likely to be correct. (cut away unnecessary complex ideas and "ad hoc" assumptions)
Outgroup
Tells us about the ancestral lineage that we compare to our ingroup taxa
- a reference taxon that branched off before
- allows us to determine (or hypothesize) what the ancestral state is.
- it's usually better to have more than 1 outgroup taxa.
Maximum Parsimony
The best tree requires the fewest changes (specific to phylogenetics rather than just the general principle)
Parsimony analysis
1. we enter all the molecular or morphological data
2. computer builds all possible trees and counts the number of steps
3. the fewest steps indicate the best phylogenetic hypothesis
Parametric (statistical) methods
Used to find best tree
- Maximum likelihood
- Bayesian inference
Both methods:
- make models on likelihood (e.g. base substitution: some substitutions are more likely than others)
- calculates how well each tree, and each branch, fits the data
- computationally demanding (Bayesian inference even more so than maximum likelihood, but some say more theoretically sound.)
Major Models of Macroevolution
- Gradualism (Theorized by Darwin, supported by Mayr)
- Punctuated equilibria (Theorized by Eldredge and Gould)
----> stasis "punctuated" by rapid change
Stephen Jay Gould
Not everything in nature is adaptive (help an organism survive)
- some features might be the byproduct of selection for other features
----> human chin seems to be a byproduct of needing small mouths and jaws
----> iridescence of golden mole fur seems to be a byproduct of needing smooth hair
- Also, some features are vestigial
AND
He co-created the model of punctuated equilibria (w/ eldredge)
Evidence used in study of Macroevolution
- Biogeography plus molecular data (e.g. chimpanzees & bonobos)
- Fossils - morphological change - transitional fossils
- Fossils - adaptive radiations after extinction events (which create opportunities for rapid evolution)
- Fossils plus molecular data: molecular clock
Molecular Clock
- some parts of the genome will accumulate changes (mutations) at a relatively steady rate
- the speed of accumulation depends on the part of DNA under study (some fast, some slow)
- the "clock" is calibrated using the fossil record (e.g. orangutan fossils have been securely dated for (the whole category of) apes), or the accumulation of mutations over generations
- Assumes that mutation rates hold steady
Example of Molecular Clock Calibration
- By using the known age of the orangutan split, plus info on orangutan DNA, we know the rate of mutations in certain parts of the ape genome.
---> count known differences in DNA between humans and chimps (to see how many mutations there have been)
- The data indicates a date of the split between Pan and Homo at about 6-8mya (million years ago).
Problems with studying the origin of life
when did it occur?
Earth is 4.5 billion years old
we know prokaryotes were around 3.5 billion years ago or more
organic molecules generally do not form fossils
Early Earth
Hadean, 4.5-4 billion years ago
- a lot of volcanism and meteors
- gradual cooling circa 4 billion years ago; water condenses and forms oceans
- early atmosphere had little to no oxygen
- lightning and uv light could have provided energy for the spontaneous production of organic molecules
Primitive Soup Hypothesis
- Tested by Miller and Urey
- Today's atmosphere is oxidizing
- Miller and Urey made an experiment with a hypothetical early atmosphere (reducing) to see if organic molecules could be produced.
- In this model, a major source of energy is from lighting and the sun
- Chromatography showed that very simple compounds had now turned into larger organic monomers (in this case, amino acids)
---> amino acids were produced in this "primitive" reducing environment
---> others have later shown that other hypothetical atmospheric compositions (neutral as opposed to reductive or oxidative) could do the same - an also produce RNA monomers and fatty acids.
Deep Sea Vent Hypothesis
- Alkaline deep sea vents could have provided energy in the form of heat and a pH gradient
- organic molecules could have formed in the pores of the vent
Volcanic Clay Hypothesis
- Volcanic clays and sun energy can also induce polymerization of macromolecules (e.g. RNA)
Water and clay environment (clay is a bit under water)
both vesicle formation and RNA polymerization happen more readily on clay surface
some experiments show replication of RNA within lipid vesicles
Protocells
the precursor of living cells
No matter which theory(s) are correct, protocells with membranes must have been formed
vesicles could have formed spontaneously (fatty acids/lipids) and water
other organic molecules (including RNA) could have been absorbed/enclosed inside the vesicles
Maintain an internal chemical environment
Origin of self-replication and evolution
- RNA molecules called ribozymes have been found to catalyze many different reactions
- Early protocells with self-replicating, catalytic RNA could have absorbed compounds from surroundings (likely on clay surface)
- some RNA copies would have been more effective at obtaining resources and would have increased in number through natural selection.
started with RNA then transitioned to DNA later because its a more stable molecule
Paleontology
Scientific study of fossil organisms (dating fossils)
Fossils (definition and types)
- preserved mineralized parts of organisms (shells, teeth, bone)
- Trace Fossils left by organisms (indirect evidence like footprints)
- Coprolites and other remains (feces)
- More rarely: soft parts preserved as minerals
- Sometimes, organisms (e.g. insects) are preserved in amber (fossilized resin from trees)
Dating Fossils
- stratigraphy (study of rock layers (strata) to understand Earth's history and relative ages. Provides framework for dating fossils)
- Relative dating: principle of superposition - older layers farther down, newer layers higher up.
- Absolute dating (chronometric): Radiometric dating
Character polarity
plesiomorphic vs synapomorphic
Principle of superposition
Older layers farther down, newer layers higher up
Absolute dating (chronometric): radiometric dating
using the known half-life of radioactive elements to estimate the age
Stratigraphy
the study of rock layers (strata) to understand Earth's history and relative ages
Examples of Radiometric Dating
1. Uranium series dating (u-series)
- uranium turns to lead
- Not 100% of it turns to lead which is why we use the half life (when its 50-50)
- Uranium is soluble in water
---> can be deposited in caves by water -> drip stone builds up with uranium, and sometimes fossils, in it -> you can see how much uranium is left to determine age.
-------> lots of times the fossil died before it was washed up into the cave (but we at least know that the fossil is older than the drip stone and uranium)
2. Argon-Argon (40Ar - 39Ar) dating is often used on volcanic rock (has a 1.25 billion year half life)
---> very accurate half life (unless super small etc. thousands of years)
3. Carbon 14 (14C) dating - 5730yr half life
---> unstable to stable carbon
---> slowly dissapears/breaks down at a steady rate
---> animals eat plants -> 14C gets into bodies -> starts breaking down
Patterns of Extinctions
Background extinctions and Mass extinctions
Background extinctions
- normal, slow rate of extinction
- 96% of extinctions
Mass extinctions
- global extent
- broad range of species
- often rapid
How many mass extinctions were there?
- 5 - some marking end of geologic eras
---> at least 5 million years to recover species diversity
- Possible current 6th mass extinction
--->1,100 species extinct since 1600 (due to habitat loss, hunting, introduction of non-native species)
- Current rate of extinction = 100-1000x larger than background extinction rate
Plate tectonics and continental drift
- movement of continents (pangaea 250mil yr ago)
- formation of mountain ranges
- leads to movement and seperation of species
- can also explain some changes in climate
First evidence of cellular life (time)
-3.5 billion years ago
- Stromatolites
3 domains:
- Prokaryotes (these occur first in the fossil record)
---> Bacteria + Archaea
---> Prokaryotes typically have a cell wall and often capsule outside the phospholipid plasma membrane
- Eukaryotes: Eukarya
First cells must have been prokaryotic autotrophs
Autotrophs: organisms that build organic molecules (like glucose) using energy from sunlight or chemical compounds.
Photoautotrophs obtain energy from sunlight (photosynthesis)
Chemoautrophs use simple compounds like ammonia NH3 (oxidizes compounds)
Heterotrophs (like animals) obtain energy from already existing organic molecules such as sugars.
Stromatolites
- the oldest known fossils
- geological structures composed of many layers of photosynthetic cyanobacteria (blue green algae, microscopic bacteria) and sediment
--->date back to 3.5 billion yrs ago
---> prokaryotes were Earth's sole inhabitants from 3.5-3 billion years ago
2.5 billion yrs ago - Atmosphere gradually saturated w/ oxygen
- many oxygen intolerant organisms died out or became confined to extreme environments (e.g. many archaeans)
- others adapted and used oxygen for cellular respiration
- atmospheric oxygen (O2) is of biological origin. the early source of O2 was likely cyanobacteria.
→O2 produced by photosynthesis reacted with dissolved iron and precipitated out to form banded iron formations
Circa 2 billion yrs ago: First eukaryotes
- oldest eukaryote cells circa 2 billion y.a.
- related to archaeans more closely than bacteria
Nuclear membrane formed from infolding of plasma membrane
- endosymbiosis: mitochondria and plastids such as chloroplasts were formerly small prokaryotes - engulfed by host cell
- mitochondria and plastids have their own DNA and replicate independently
1.5 bil y.a. - multicellular eukaryotes
- Oldest known fossils of multicellular eukaryotes = tiny multi-cellular algae (photosynthetic protists) from 1.5 bil y.a.
- More diverse multicellular organisms do not occur until around 600 mil. y.a. (precambrian era)
Early Animals
- Enigmatic precambrian (ediacaran) fossils
- some are hard to identify as either animals or algae - but some have trace fossils
- some are definitely the earliest animals ca 600 mil. y.a. (no vertebrates)
Animals (__ genes)
Earliest animals ca 600 mil. y.a. - so a peculiar genetic mechanism must have evolved by then:
- Homeotic genes containing a highly conserved (virtually unchanged across evolution) 180-nucleotide "Homeobox" are called Hox genes; always found in animals
---> code for the position of anatomical parts along body axis in animals, and is one of the oldest animal synapomorphies
---> the position of Hox genes along the chromosome is the same as the position of expression along the body axis
Paleozoic Era Starts ~ 550 mil ya: Cambrian explosion
- Many modern animal phyla suddenly appear
- Most of life is still in the seas, but some plants and invertebrates are found on land shortly after
- first fossil chordates and vertebrates
---> best preserved in Burgess Shale, Canada
---> sudden appearance of fossils resembling modern phyla
---> provides the first evidence of predaor-prey interactions
------> more armor (shells, spikes)
Chordates
- form a monophyletic taxon - with vertebrates being the most numerous group
---> chordate shared characters (synapomorphies): notochord (beginning of backbone) and myotomes (skeletal muscles)
Ancient Chordates - Cambrian relatives of the modern vertebrates
- chordates similar to the lancelet (modern chordate) are known from the cambrian 530 mil ya Burgress Shale + China (e.g. Pikaia and Haikouella)
- have the typical chordate features: notochord and myotomes
Typical chordate features
notochord (beginning of backbone) and myotomes (skeletal muscles)
Late Cambrian (ca 500 mya): Conodonts - The first Jawless "Fish"?
- Among the first true vertebrates - probably had vertebral column made from cartilage, replacing notochord
- Jawless (agnathan) but with a strange apparatus of mineralized teeth in mouth
- Extinct today but conodont dental elements are often plentiful in fossil strata (used in stratigraphy)
Paleozoic continues - Gnathostomes
- Gnathostomes are vertebrates with true jaws supported by skeleton, first apprearing ca 450 mya (ordovician-silurian)
- Placoderms were among the earliest gnathostomes - highly armoured with bony plates
- some were large top predators 20ft long
Devonian (middle of Paleozoic: 420-360mya)
- The devonian "age of fish"
- Gnathostomes diversify into numerous "fish" groups - includes placoderms, cartilaginous fish (chondrichthyans) and bony fish (osteichthyans)
- Bony fish of the Devonian include lobe-fins (sarcopterygii, similar to modern coelacanths and lunch fish)
Sarcopterygians have many tetrapod like features including robust bones in the appendages (fins).
In a lineage of sarcopterygians, fins became progressively more limb-like: evolve into tetrapods, vertebrates walking on land
- Early tetrapods: many more digits (fingers and toes) than modern tetrapods, but the bones in the limbs were otherwise the same: e.g. humerus, radius, ulna.
Later Devonian Origin of Tetrapods
- Some sarcopterygians (like tiktaalik) had fins with limb-like skeleton
---> e.g. the pectoral fin (forelimb) of Tiktaalik has a humerus, radius, and ulna
- Acanthostega was a basal tetrapod with full limb skeleton and lots of digits (but with gills - still spent most time in water)
Sarcopterygians
a major monophyletic clade of vertebrates defined as the lobe-finned fishes and all of their tetrapod descendants (including amphibians, reptiles, birds, and mammals).
Paleozoic (still devonian): Early Tetrapods
developed "amphibious" life cycle; reproduction similar to modern amphibians.
- modern amphibians still lay eggs and have larval stages in water - then metamorphosis
Paleozoic: Carboniferous (360-300 mya) - Amphibians diversify
- Early tetrapods gave rise to several groups with amphibian life cycle (egg + larvae in water, adult on land)
- some amphibians were much larger than modern forms
---> a "reptiliomorph" group of amphibious tetrapods gave rise to amniotes (major group of tetrapod vertebrates that are able to reproduce on land using an amniotic egg)
- hot and humid climate
Tetrapods
Google: four-limbed vertebrates and descendants of four-limbed ancestors, encompassing amphibians, reptiles, birds, and mammals
Carboniferous - the earliest amniotes
- early amniotes are present in the carboniferous - these looked superficially like modern lizards (so some people inaccurately called them "reptiles"
- Amniotes such as Hylonomous had relatively large eggs that could be laid on land - no larval stage in water
- the amniote egg has extraembryotic membrane with four layers: amnion (amniotic fluid), yolk sac (nutrient), chorion (gas exchange), allantois (disposal of waste product)
- Early amniotes gave rise to two groups in the Carboniferous: reptiles (Reptilia (e.g. hylonomous): radiated into many groups) and synapsids (synapsida; today only mammals)
Reptiles
- Lepidosaurs today include lizards and snakes etc.
- Archosaurs include crocodilians, birds (and extinct dinosaurs)
- Turtles are a highly specialized group of reptiles that appear later in the fossil record
- Reptiles skulls can often be recognized by having two temporal fenestrae
Synapsida
The evolution of mammals from basal synapsids (such as dimetrodon) is one of the best understood transitions in fossil record (very well preserved)
- major lineage of amniote tetrapods
- Synapsids have 1 temporal fenestra
---> Dimetrodon, cats, humans
- Dimetrodon is a basal synapsid; more advanced forms include therapsids (such as cynodonts) and mammals
Permian: Synapsida Diversify
- Final era of Paleozoic
- Members of synapsida become numerous during the permian
- Therapsids (a mammal like group of synapsids) become common
Permian mass Extinction
- end of Paleozoic
- About 250mya
- Perhaps caused by massive volcanism
- Synapsida takes a big hit, but some therapsids survive the Great Permian Extinction event.
Permian - 300-250mya (what era? what animals? what climate? what geography?)
- Toward the end of the Paleozoic
- Continents collect together to form Pangea
- Hot and dry climate in many places
- Diversification on land: Synapsida very common (e.g. Dimetrodon, therapsids), but also many reptiles diversifying (Lepidosaurs, archosaurs)
Mesozoic Era
- ca 250-65 mya
- Continental drift
---> Triassic: Still Pangea (single continent), still hot and dry
---> Late Jurassic - Early Cretaceous: Seperate continents, more humid (still warm)
Triassic
- Mesozoic ("The age of reptiles")
- Archosaurs (within reptilia) were particularly important in the Triassic, giving rise to the earliest crocodilians, pterosaurs, and dinosaurs
- Dinosaurs were originally small and bipedal
- Mammals (within synapsida) also evolved at this time, but remained small and mostly nocturnal.
Jurassic + Cretaceous
- Mesozoic (age of reptiles)
Dinosaurs dominate terestrial faunas
- Dinosaurs diversified greatly in the late Triassic, continuing into the Jurassic and Cretaceous
- Many were bipedal e.g. the carnivorous theropods, such as Tyrannosaurus and Allosaurus
- Some quadrupedal (usually herbivores) e.g. Sauropods
- Many were very large, but small dinosaurs (chicken size and upwards) were always common throughout this age
Sauropod dinosaurs reach maximum size
- weight estimates are hard to calculate, but some South America sauropods may have reached 80 metric tons (abt 10 large African elephants)
Theropod dinosaurs give rise to birds
- many dinosaurs had a layer of "fluff" in addition to scales. In some, this has been identified as feathers
- A group of small feathered therapods gave rise to birds in the jurassic
---> Archaeopteryx is an early example (had airfoil shaped feathers on its wings, but also dinosaur like teeth, claws and tail.
Around 160mya many mammalian groups evolve, including 3 extant groups:
- Monotremes (reproduce with egg)
- Marsupials (pouch)
- Placental mammals (placenta)
Cretaceous Mass Extinction - end of Mesozoic
- ca 65-66mya, end of mesozoic, beginning of cenozoic
- Asteroid impact in Mexico, repercussions felt all over the world
Other Mesozoic Reptiles (not dinosaurs)
- The mesozoic also had many non-dinosaurian reptiles in other niches e.g. plesiosaurs and ichthyosaurs in seas, and flying pterosaurs.
Mesozoic Synapsida
Therapsids continued to evolve, but were smaller and more mammal like in the Triassic (eg Cynodonts)
Therapsids to Mammals (facial structures)
- Early synapsids (paleozoic) had a primitive Jaw Joint (hinge) made from the quadrate and the articular bones.
- There were many bones in the lower jaw (the biggest being the dentary) and all the teeth look the same (as in reptiles). The only bone in the middle ear is the stapes.
- This jaw joint became reduced and more slender in later therapsids - it is possible that the animals could sense vibrations through it.
- In more advanced therapsids (cynodonts) the dentary articulates with the skull directly - as in mammals. The articular and quadrate bones are still attatched to the jaw but have become part of a hearing system.
in mammals, the articular and quadrate bones have become detached from the jaw, and are now the malleus (articulate) and incus in the middle ear.
- In mammals, there is only one bone left in the lower jaw - the dentary (usually called mandible in humans)
- Also in mammals; the teeth are specialized/differentiated (incisors, canines, premolars and molars)
Mesozoic Mammals
- Advanced therapsid synapsids (cynodonts) gave rise to mammals about 200 mya (triassic-jurassic)
- Brain expanded
- Highly active and endothermic (warm blooded); the new hearing system is very sensitive to a wide variety of frequencies, and the larger brain enhanced the ability to learn.
- The first mammals were small and mainly insectivorous (e.g. Morganucodon)
---> similar to modern opossums of shrews - but laid eggs
- existed at the same time as dinosaurs (throughout the Jurassic and Cretateous)
---> Mammals have larger brains than dinosaurs
Cenozoic Climate Changes
warm and humid early on, cooler drier, and more variable later: glaciations
Primate Origins
Primates include lemurs, monkeys, and apes
Most are adapted for climbing trees and eating fruits: have opposable thumbs
Brain is larger than most other mammals
Molecular clock suggests Mesozoic origin, while fossils indicate they evolved later
Darwinius (45 mya) is an example of a complete early primate fossil, but fragments of the group are found much earlier
The fossil record of most apes is relatively poor
lots of confusion about origin of apes
Hominins
Species that are more closely related to Homo sapiens than to chimps/bonobos
After the split, about 7mya (Last common ancestor), there were several breaks on the human (hominin) tree.
Many fragmentary fossils
the first fossils in our lineage that are fairly well understood: Ardipithecus
First typically human trait to occur: bipedalism
Ardipithecus spp.
Australopithecus spp.
“Robust” Austr.
H. habilis
H. ergaster/erectus
H. neanderthalensis
H. sapiens
Ardipithecus (2 spp) 4-5mya, East Africa
the first Hominin fossils in our lineage that are fairly well understood: Ardipithecus
Skull very chimp-like, but foramen magnum is directly underneath skull (rather than behind)
Shows standing upright not on all fours
Human-like pelvis - almost certainly a (partial? mostly?) bipedal
shape supports their top half
Could still climb well
Australopithecus spp. (e.g. “Lucy”) 2-4mya, Africa, several species
Skull chimp-like, but foramen magnum is directly underneath skull (just like Ardipithecus)
“Lucy” is a famous example
some evidence of stone tool use
certainly walked on two legs (bipedal)
footprints found in volcanic ash
Side branch: “Robust Australopithecus” (paranthropus) spp
“Robust Australopithecus” (Paranthropus)
Side branch of Australopithecus
2-3mya, Africa
Skull is chimp-like, but wide and robust - powerful jaw musculature
Rest of the skeleton like Australopithecus
Ate roots int eh dry season (?)
A hominin side branch that died out
When did the genus “Homo” evolve?
ca 2 mya
Homo habilis
Around 2mya (2.5-1.5), Africa
Lots of evidence of stone tool use
Skull with markedly larger braincase (between Australopithecus and modern humans)
climate shifts in African involved?
If climate is shifting back and forth → maybe they need a larger brain to learn to adapt.