evolution exam 4

what are the two main sources that inform out understanding of life’s history

1. Fossils: reveal extinct organisms and past events, though the fossils record is incomplete and often missing soft-bodied species or traits like behavior or physiology

2. living organisms: provide genetic, morphological, and behavioral data used to reconstruct phylogenetic trees and infer evolutionary relationships

what are phylogenetic trees crucial for

• Interpreting fossils and identifying

evolutionary connections (e.g., dinosaurs

and birds).

• Classifying organisms meaningfully based on

evolutionary history.

• Testing hypotheses about evolutionary

processes

phylogeny

Evolutionary history showing relationships among species.

Derived vs. ancestral characters:

• Derived (synapomorphy): Newly evolved

trait shared by species from a common

ancestor (e.g., hair).

• Ancestral: Traits inherited from distant

ancestors (e.g., tails in vertebrates)

Monophyletic group (clade)

Species sharing a most recent common ancestor (MRCA).

Outgroup

A more distantly related species used to determine the direction of evolutionary change.

Inferring Relationships

•Shared derived traits (synapomorphies) indicate common ancestry.

•Traits that evolved only once provide stronger evidence for relationships.

Parsimony principle

Choose the tree requiring the fewest evolutionary changes.

Challenges in Estimating Phylogenies

1. Homoplasy (Independent Evolution of Similar Traits)

•Arises from convergent evolution, parallel evolution, or evolutionary reversal.

•Causes unrelated species to appear similarwithout shared ancestry.

•Example:

• Winglessness in fleas, lice, and some crickets evolved independently.

•Including many characters and species reduces errors caused by homoplasy.

2. Multiple Substitutions in DNA

• The same nucleotide site can mutate repeatedly (A→C→T→A), masking evolutionary history.

• Long branches (old lineages) accumulate many substitutions, reducing clarity.

• Use slowly evolving genes for deep-time relationships and faster-evolving genes for recent divergences.

• Example: Second codon positions evolve slower than third positions.

3. Rapid Diversification (Adaptive Radiations)

• Short intervals between speciation events →few mutations fixed → hard to resolve relationships.

• Leads to Incomplete Lineage Sorting (ILS):

• Gene trees differ from species trees because ancestral genetic variation persists across speciation events.

• Causes conflicting phylogenies among genes.

• Common in rapid radiations (e.g., birds, mammals, flowering plants).

4. Introgression (Gene Flow Between Species)

•Exchange of genes across species boundaries distorts phylogenies.

• Hybridization: Common in eukaryotes.

• Horizontal Gene Transfer (HGT): Common in prokaryotes; early life resembled a network, not a simple tree.

•Example: Anopheles mosquitoes show conflicting gene trees due to hybridization; X chromosome retains the true species tree.

Most modern phylogenies are based on?

DNA or genomic data

Parsimony method

• Chooses the tree with the fewest evolutionary changes (least homoplasy).

• Works well in some cases but fails when there is high homoplasy or uneven evolutionary

rates

Statistical Approaches

• Maximum likelihood (ML):

• Uses probability theory and assumptions (e.g. Molecular clock).

• Finds the tree and substitution rate that maximize the likelihood of observed data.

• Bayesian inference:

• Similar to ML but incorporates prior information (e.g., fossil dates).

• Handles large or complex datasets better than ML.

Statistical Approaches advantages and limitations

Advantages of Likelihood & Bayesian Methods:

• More robust to homoplasy.

• Estimate branch lengths and support values for trees.

• Can estimate additional parameters (e.g., substitution rates).

• Widely used in modern phylogenetics.

Limitations:

• Can yield incorrect results if assumptions are wrong.

• Harder to apply to morphological data.

• Often computationally intensive.

Bootstrapping:

• Randomly resample data and re-estimate phylogeny multiple times.

• Consistent results across replicates increase confidence.

Phylogenies from Phenotypes

• Historically based on morphological traits before DNA data became available.

•Still crucial when DNA is unavailable, especially for fossils.

•Requires careful identification of derived vs. ancestral traits

Example: Birds as Theropod Dinosaurs

•Birds belong to the theropod clade (dinosaurs).

•Shared derived features:

• Reduced fibula, backward-pointing pubis, fused clavicles (furcula).

• Hollow bones and air sacs.

• Three-fingered hands with similar digit structure.

• Feathers present in many theropods.

•Fossils like Archaeopteryx, Microraptor, and Anchiornis show transitions between dinosaurs

and birds.

•Feathers likely evolved for insulation or display before flight.

How do we use phylogenies? what are the uses of phylogenies

• Reveal relationships among species.

• Date evolutionary events.

• Study gene evolution.

• Investigate adaptations.

• Classify species based on evolutionary

history

how do we use phylogenies? Dating evolutionary events

• Molecular Clock Concept:

• DNA differences accumulate roughly at aconstant rate.

• Enables estimation of when species diverged.

• Tests for Constancy:

• Fossil calibration: Plot sequence differences vs. fossil-based divergence times; a linear relationship indicates constant rates.

• Observed Rate Differences:

• Slower sequence evolution in humans →primates → rodents → plants (herbaceous faster than woody).

• Often linked to generation time—shorter generations → faster evolution.

How do we use phylogenies? Discovering the history of genes and cultures

Example: Stickleback Fish (Eda gene):

• Freshwater populations repeatedly evolved low armor plating.

• Same Eda allele found in both Atlantic and Pacific populations → adaptation from standing genetic variation.

Cultural Phylogenies:

• Linguists use phylogenetic methods to reconstruct language and cultural evolution.

• Austronesian societies: Language-based phylogeny shows gradual increases in political

complexity, with some reversals.

• Demonstrates that phylogenetic tools can study non-genetic (cultural) evolution

how do we use phylogenies? reconstructing ancestral states

Phylogenies help infer ancestral traits:

• Example: Mammals’ common ancestor was quadrupedal; humans’ lineage evolved bipedalism later.

how do we use phylogenies? Tracing geographic and epidemiological history

Phylogenies track spread of species or pathogens.

Ebola Virus Case Study:

• Gene tree traced 2014 outbreak to a single ancestral infection in West Africa.

• Showed all epidemics descended from one spillover event, not repeated environmental jumps.

Studying adaptations: the comparative method

• Purpose: Tests adaptive hypotheses by comparing traits across species.

• Basis: Uses convergent evolution as evidence that similar traits evolved independently under similar selective pressures.

• Example:

• Bergmann’s rule: Larger body size in colder climates → adaptation for heat conservation.

• Long, slender bills in unrelated nectar- feeding birds (hummingbirds, sunbirds)

→ adaptation for feeding from tubular flowers.

Helps to Test adaptive hypotheses

• links ecological factors to traits evolved in multiple lineages

• allows testing of prior hypotheses

Testing evolutionary correlations between traits

• used to see if two traits evolved together

what is the purpose of classification

helps to organize and communicate about diverse organisms

• early organisms were grouped via observable traits, not evolutionary relationships

• pre Darwin classifications lacked an objective genealogical basis, so “relatedness” was metaphorical

Darwin’s contributions to classification

redefined classification as genealogical and reflecting shared ancestry

what are monophyletic groups

also known as clades, it is an ancestor to all its descendants

• modern taxonomy aims to recognize only monophyletic groups

non- monophyletic groups

1. paraphyletic group: includes ancestor and some, but not all, descendants

2. polyphyletic groups: includes species from different ancestors; excludes their true common ancestor

what are modern phylogenetic classification systems

1. evolutionary relationships, not just surficial similarities

2. monophyletic taxa

3. convergent evolution can mislead classification if phylogeny isn’t considered

what are challenges in classificaiton

1. taxonomic ranks have arbitrary boundaries: lumpers vs. splitters

2. extinct only taxa can be paraphyletic if living descendant are excluded

• crown group: living descendants and their last common ancestor

• stem group: extinct relative outside the crown group

how long ago was early life and what did it consist of

3.5 billion years ago and bacteria like prokaryotes

what two ways were the evolutionary record inferred

1. phylogenetic inferences

2. fossils providing direct evidence and absolute time scale

key patterns in evolutionary history

1. interactions: living things have affected earths atmosphere

2. change: earths climates have continually changed

3. diversity: the way things shift over time has created a variety of new habitats

4. extinction and diversification: mass extinctions lead to rapid diversification

Rock formation of Igneous rock, sedimentary rock, and metamorphic rock

1. Igneous rock: cooling magma extruded from deep within the earth

2. sedimentary rock: deposition and solidification of sediments. MOST FOSSILS ARE FOUND IN THIS TYPE

3. metamorphic rock: alerted igneous or sedimentary rock due to high temperature and pressure

Plate tectonics ( the lithosphere)

• consist of plates that move over the plastic asthenosphere at 5- 10 cm/year

• movement is driven by convection currents in the asthenosphere where rising magma forms new crust and pushes plates apart

• collision between plates causes subduction

What is an absolute age

form of radiometric dating that looks at radioactive parent elements

• in igneous rock the ration of these atoms estimates the rock’s age based on the half-life of the element

• sedimentary rock is estimated by the igneous formations above or below

what are relative ages

principle that younger strata are on top of older strata

how are geological eras and periods recognized

by distinctive fossil taxa

what eon did animals appear and become diverse

phanerozoic

the phanerozoic eon is divided into three eras what are they and what are they characterized by

Paleozoic era: stars 541 ma, Cambrian period

Mesozoic era: starts 252 MA, triassic period

cenozoic era: starts 66 MA, paleogene period

how much of the fossil record is incomplete and why

only about 250,000 described fossil species so less than 1% of species that have lived

• organism type leads to delicate or lack of hard parts

• episodic disposition sporadic capturing of fragments over time

• preservation and accessibility

Timeline of early earth

Universe was formed 14 BYA

solar system was formed 4.6 BYA

oceans formed possibly 4.5 BYA

what are the challenges in studying life’s origins

• no historical record

what are the leading hypothesizes for pre-life chemistry

• Cradle of Life: May have been hydrothermal vents (3.8 Ga), where heated, chemically-rich water mixes with seawater.

• Metabolic Reactions: Vents provide energy and catalysts (from reduced chemicals like hydrogen, sulfur, and iron) to drive the reduction of CO2 into complex organic compounds (amino acids, lipids, ribonucleic acids).

• First Step: A disorganized collection of molecules concentrated and synthesized more complex molecules using the vent's chemical energy.

Evidence for a single common ancestor (LUCA)

• Once a self-replicating, energy-harvesting chemical system arose, life existed. Though multiple origins are possible, all current life descends from a Last Universal Common Ancestor (LUCA), possibly living as early as 4.5 Ga.

• All known life shares several key homologies inherited from LUCA, strongly indicating a

single origin:

• DNA as the basis of inheritance.

• A "universal genetic code".

• Cells enclosed by a lipid bilayer.

• ATP used for energy storage

Pre cambrian period

The Precambrian period includes the Archean (before 2.5 Ga) and the Proterozoic

(2.5 Ga to 541 Ma).

Early Life:

• The Last Universal Common Ancestor (LUCA) is estimated to have existed around 4.5 Ga.

• Strong fossil evidence of life, including bacteria-like microfossils and layered mounds called stromatolites (formed by cyanobacteria), dates back to 3.8 Ga

prokaryotic dominance and diversification

for over 3 billion years earth only had prokaryotes, they started diversifying due to metabolic capacity and lateral gene transfer

transformation of earth by photosyntesis

early organisms were anaerobic, photosynthesis in cyanobacteria introduced oxygen into the atmosphere around 3.5 Ga, the first increase in oxygen was the great oxidation event about 2.4 Ga and allowed the rise of aerobic respiration and more complex multicellular organisms

early eukaryotes

• defined by nucleus, cytoskeleton, mitochondria, chloroplast, and undergoing meiosis

• were endosymbionts (archaea that engulfed bacteria)

• first found about 1.65 GA

• for the first billion years of life almost all were unicellular protists

multicellularity

multicellularity allowed the division of labor between cell types

pre-Cambrian animals (Proterozoic eon)

Ediacaran fauna: soft bodies, flat creature that lacked hard parts, mouthparts, or locomotory

Molecular vs. Fossil Evidence:

• Molecular Data: Phylogenetic studies using DNA divergence suggest the common ancestor of all living animals existed more than 700 Ma (well before the Cambrian), with sponges and

cnidarians forming distinct lineages long ago.

• Fossil Record (The Conundrum): Except for sponges, no living animal phyla are recorded in the fossil record before the start of the Cambrian Period (541 Ma).

the closest relatives of animals are what

unicellular choanoflagellates, resemble cells of sponges

The cambrian explosion

began in the Paleozoic era and started with low animal diversity but almost al modern phyla and classes of skeletonized marine animals suddenly appeared in the fossil records. Marking the appearance of mollusks, echinoderms, and arthropods and the most dramatic adaptive radiations in life’s history.

possible causes of the cambrian explision

• ecological shifts: involved evolution of hard parts and novel ways of living like predation and burrowing

• environmental factors: increase in atmospheric oxygen

The Paleozoic era (541-252MA)

saw immense diversification, early vertebrates in this era had no jaws or limbs

the Ordovician diversification and extinction: many animals diversified but the era ended in a mass extinction likely caused by a drop in global temperature and sea level.

then jawed vertebrates became common in the Silurian and Devonian eras

then plants colonized land ( embryophyta) evolved from green algae and then vasular plants evolved by the silurian

also saw terrestrial arthropods

the end Permian mass extinction

triggered by volcanic eruptions in Siberia and large amounts of carbon dioxide

mesozoic life: The age of reptiles

divided into the Triassic, Jurassic, and cretaceous periods

• Pangea began to split and the overall climate was warm

• marine life slowly started to recover from the end-Permian extinction and resulted in the Mesozoic marine revolution where hard shells and bony fished evolved

• flora was dominated by gymnosperms and angiosperms diversified rapidly in the mid cretaceous

• reptiles ( diapsids) became very diverse

• all dinosaurs were extinct by the end of the cretaceous except for a single group that we now know as birds

• mammals (synapsid) diversified late Triassic and early Jurassic

• the end- cretaceous (k/pg) mass extinction 66mya lead to the extinction of the last no avian dinos, from asteroid at the chicxulub crater