Bio 140 Handout II. Patterns and Evidence of Evolution

Domestication

• shows evolution in action

• demonstrates how populations change over time under selective pressures

  • human preference

  • artificial selection

• Shows that species can change over time

domestication

___________ is similar to natural selection as it uses artificial selection, its controlled evolution.

hybridization

______________ may also be performed in domestication, not only narrowed, controlled evolution towards a specific ideal.

• Diet not easily supplied by humans like in ant eaters

• slow birth rate and long birth spacing like in elephants

• Reluctance to breed in captivity like in pandas

• Lack to follow-the-leader dominance hierarchies like in rams

• Tendency to panic in enclosures like in gazelles

• nasty disposition (too mean or wild)

What are the reasons some animals can be domesticated?

Evolutionary arms race

It is an evolutionary struggle between competing sets of co-evolving genes, traits, or species, that develop adaptations and counteradaptations against each other

Homology

It is the same structure is seemingly modified to various forms to suit different adaptive functions

Homology

It is strong evidence of common ancestry

Analogy

These are functionally similar features that differ profoundly in structure

Analogy

Caused by different ancestors adapting to similar niches

Stabilizing Selection

Patterns of Natural Selection

- Intermediate phenotypes are favored.

Stabilizing Selection

Patterns of Natural Selection

- Extremes are selected against.

Directional Selection

Patterns of Natural Selection

One extreme phenotype is favored.

Disruptive/Diversifying Selection

Patterns of Natural Selection

Both extremes are favored over intermediate phenotypes

Extinction and Radiation

Patterns of Macroevolution

- Mass extinctions wipe out lineages, opening niches for surviving groups to diversify.

Stasis

Patterns of Macroevolution

- Evolutionary change happens slowly and steadily over long periods of time.

Adaptive radiation

Patterns of Macroevolution

- Rapid diversification of a lineage into many niches

Vestigial traits

- features that were useful in ancestors but lost their original function

Vestigial traits

They may still:

• have no function (remnants)

• evolve new uses (co-opted)

Vestigial traits

Example: Ostrich wings — can't fly anymore but help with balance, mating, shade, and defense

What are examples of human Vestigial traits?

Atavisms

Recurrence of an ancestral trait that disappeared after being unexpressed for many generations

Atavisms

Rarely appear at an individual level; must be expressed in the exact same way as it was in its ancestor

Atavisms

Hypothesized that these genes were once functional, and later became dormant due to natural selection

Pseudogenes or Dead Genes

A _____________ is a segment of DNA that structurally resembles a gene but is not capable of coding for a protein.

Pseudogenes or Dead Genes

_______________ are most often derived from genes that have lost their protein-coding ability due to accumulated mutations that have occurred over the course of evolution.

Pseudogenes or Dead Genes

This shows evidence that common ancestry exists, as even the dead genes, much like regular genes, share a time-dependent similarity between close relatives.

The GLO (L-GULONO-Y-LACTONE OXIDASE) gene in chimps and humans is more similar compared to that of guinea pigs, even though both mutations cause the inability to produce vitamin C; in the latter, it's more different due to it evolving independently.

Palimpsests

As development continues, early structures transform, disappear, or rearrange, showing traces of earlier evolutionary stages rather than forming as a “tiny human.”

Palimpsests

Darwin explained these patterns as evidence of common ancestry, comparing embryos to a __________, a manuscript written over with new text while still leaving fragments of the old writing visible beneath.

Palimpsests

Palimpsests

Karl Ernstr von Baer

German embryologist, “Father of Embryology”

Ernst Haeckel

“German evolutionist. Formulated a “biogenetic law” in 1866, famously summarized as “Ontogeny recapitulates phylogeny.”

Bad design

____________ holds that if organisms were created from scratch, they would be free of flaws. Instead, evolution modifies and reuses existing structures, so new traits must work with older ones, often resulting in imperfections

Bad design

____________ refers to biological traits that seem inefficient, not because they were purposefully engineered that way, but because evolution works by modifying existing structures instead of creating flawless designs from scratch.

Fossils

These are preserved remnants or impressions left by organisms that lived in the past

Fossil Record

It is an ordered array in which fossils appear within layers or strata of sedimentary rocks

~250,000 described fossil species – ~1% of the species that lived in the past

Body fossils

Types of Fossils

– direct remains of the organism

Body fossils

Types of Fossils

Bones and Teeth – most common in vertebrates

Body fossils

Types of Fossils

Shells and exoskeleton – common in invertebrates

Body fossils; petrified wood

Types of Fossils

Leaves and wood – plant fossils including ____________ (organic material has been replaced with minerals)

Body fossils

Types of Fossils

• Hair, skin, and feathers – rare; delicate

Body fossils

Types of Fossils

Preserved organisms

• Amber fossils – eg. insects in tree resin

Body fossils

Types of Fossils

Preserved organisms

• Fossils in glacial ice caps – eg. frozen mammoths

Body fossils

Types of Fossils

Preserved organisms

• Exceptionally preserved fossils – have soft tissues preserved

Trace fossils

Types of Fossils

indirect evidence of an organism’s presence and behavior

Trace fossils

Types of Fossils

Footprints and tracks – impressions by animals

Trace fossils

Types of Fossils

Burrows and borings – holes or tunnels in sediments or wood

Trace fossils; Coprolites

Types of Fossils

____________ – fossilized feces

Trace fossils; Gastroliths

Types of Fossils

______________ – stones swallowed by animals, often polished smooth inside the gastrointestinal system then fossilized

Preservation without alteration; dehydration

Methods of fossilization

by __________ eg. animal remains in extremely dry conditions (as in deserts) and in caves

Preservation without alteration; burial; sediments

Methods of fossilization

by _________ in __________ ~ hard parts

• Organic – bone, cartilage, chitin (exoskeleton)

• Inorganic – tricalcium phosphate, calcium carbonate (corals and mollusks), silica (sponges, diatoms, protozoans)

Preservation without alteration; mummification; amber; acid bog; tar pit

Methods of fossilization

through ____________

• Imprisonment in ice

• Preservation in _________

• Preservation in an ___________

• Preservation in a __________

Preservation with alteration; Petrifaction

Methods of fossilization

___________ – organic parts hardened to stone; occurs usually where there is abundance of mineral-containing water

Preservation with alteration; Carbonization

Methods of fossilization

______________ – hard parts become carbonized or a film of carbon is left as impression

Preservation with alteration; Mold

Methods of fossilization

Formation of replicas

• ___________ – imprint of external or internal form of the skeleton or body part

Preservation with alteration; Cast

Methods of fossilization

Formation of replicas

• __________ – replica of organism formed when skeletal or body parts are dissolved and the mold is filled with sediments
  
  

Preservation with alteration; Trace fossils

Methods of fossilization

Formation of replicas

• ______________ - tracks, burrows, coprolites
  
  

Sand; silt; rivers; pile up; compress; sediments; strata; sedimentary; Erosion

Formation of fossils

1. _______ and _______ are carried by _________ to seas and swamps.

2. Deposits ________ and _______ other sediments below into rock.

3. When organisms die, they settle along with the ________; a tiny fraction is preserved as fossils.

4. Over time, additional _______ are added, containing fossils from each time period.

5. As sea levels change and the seafloor is pushed upward, _________ rocks are exposed.

6. __________ by rivers reveals strata; older strata contain older fossils.

sedimentation; solidification; persistence; exposure

Gaps in fossil records

1. Many kinds of organisms rarely become fossilized because they are delicate, lack hard parts, or occupy environments where decay is rapid (eg. humid forests).

2. Sediments generally form in a given locality very episodically, containing only a small fraction of species that inhabit a particular locality.

3. Fossil formation and eventual discovery require several events to occur:

   • → s___________

   • → s___________ into rock

   • → p___________ of the rock without being eroded, metamorphosed or subducted

   • → e___________ of the rock

   • → discovery by paleontologists

4. Evolutionary changes may not occur at a locality conducive for fossilization.

Relative Dating

Methods of Dating Fossils

(Also state the subtype of method if applicable)

- Uses fossils in each stratum of sedimentary rock

Relative Dating

Methods of Dating Fossils

(Also state the subtype of method if applicable)

- Compare or correlate the strata at one location and at another location by the presence of similar fossils called – “index fossils”

Absolute Dating; Radiometric dating

Methods of Dating Fossils

(Also state the subtype of method if applicable)

- Fossils contain isotopes of elements that accumulated in the organisms when they were alive

Absolute Dating; Radiometric dating

Methods of Dating Fossils

(Also state the subtype of method if applicable)

- Unstable isotope – decays into a different element exponentially

Absolute Dating; Radiometric dating

Methods of Dating Fossils

(Also state the subtype of method if applicable)

- Half-life of a radioactive isotope – the time taken for half of its atoms to decay

Absolute Dating; Measuring the rate of racemization; Racemization

Methods of Dating Fossils

(Also state the subtype of method if applicable)

- _____________ – interconversion of levorotatory (L) and dextrorotatory (D) enantiomer amino acid forms

Absolute Dating; Measuring the rate of racemization

Methods of Dating Fossils

(Also state the subtype of method if applicable)

- living organisms- have L- a.a.; dead organisms- mixture of L- and D- forms (in soils and sediments)

Absolute Dating; Measuring the rate of racemization

Methods of Dating Fossils

(Also state the subtype of method if applicable)

- one can determine how long the organism has been dead based on the rate of racemization

11,460 years old

Sample Problem: The half-life of carbon-14 is 5,730 years. If a specimen sample had 25% of carbon-14 in today’s environment, how old would is the sample?

Biogeography

The study of the world (or geographic) distributions of organisms

Historical biogeography

The main difference between ecological and historical biogeography is the time-scale one. While ecological biogeography searches causal explanations of the distributional patterns in short temporal scales, historical biogeography concerns evolutionary processes over millions years (Crisci, 2001).

One example is the closing of an ocean barrier previously separating two continents, such as the Turgai Strait between Europe and Asia 30 million years ago, which led to episodes of range expansion occurring simultaneously in multiple animal clades

Two components of Biogeography

– certain distributions of organisms are the consequences of long-term evolutionary history

Ecological biogeography

The main difference between ecological and historical biogeography is the time-scale one. While ecological biogeography searches causal explanations of the distributional patterns in short temporal scales, historical biogeography concerns evolutionary processes over millions years (Crisci, 2001).

Two components of Biogeography

– organisms’ distributions are the result of ecological factors operating at the present time

Biogeographic Pieces of Evidence

1. Diversity is not entirely accounted for by climate and environment.

2. Geographical barriers can be factors in formation of various species.

3. The plants and animals of each continent are distinctive; within each continent, organisms tend to be more related.

4. Island-continent relation: Species on oceanic islands show strong affinities to those on the nearest mainland.

5. Although oceanic islands have few species, those they have are often unique (endemic) and show relatedness to one another.

Biogeographic Pieces of Evidence

1. Diversity is not entirely accounted for by climate and environment.

2. Geographical barriers can be factors in formation of various species.

3. The plants and animals of each continent are distinctive; within each continent, organisms tend to be more related.

4. Island-continent relation: Species on oceanic islands show strong affinities to those on the nearest mainland.

5. Although oceanic islands have few species, those they have are often unique (endemic) and show relatedness to one another.

1. Endemic

2. Cosmopolitan

3. Disjunct

Major Patterns of Distribution

1. __________ – limited to a certain region

2. __________ – found on all continents

3. __________ – when some taxa have gaps in their distribution

1. Extinction

2. Vicariance

3. Dispersal

https://www.zoology.ubc.ca/~jankowsk/BIOL413-7-011518-Dispersal.pdf

Events/Factors Influencing Distribution

1. __________
   

2. __________ – separation of populations of a widespread species by barriers arising from changes in geology, climate, or habitat; results in divergence to different subspecies, species, or higher taxa
   

3. __________ – when members of a species move and expand their range

   • range expansion

   • jump dispersal

Biogeographical observations across Continents

1. Species that live in similar habitats will experience similar selection pressures from their environment, so they may evolve similar adaptations or convergence, coming to look and behave very much alike even though they are unrelated.

2. Species living in one area should be the descendants of earlier species that lived in the same place.

Biogeographic realms

______________ - inhabited by many characteristic higher taxa

• → taxonomic composition of the biota is more uniform within certain regions than between them

Biogeographic realms

- Wallace designated these realms for terrestrial and freshwater organisms

• → still widely recognized today

1. Palearctic

2. Nearctic

3. Ethiopian

4. Oriental

5. Australian

6. Neotropical

Biogeographic realms

1. P_________ – temperate & tropical Eurasia and Northern Africa

2. N_________ – North America

3. E_________ – sub-Saharan Africa

4. O_________ – India and Southeast Asia

5. A_________ – Australia, New Guinea, New Zealand, & nearby islands

6. N_________ – Central and South America

Taxonomy

Phylogeny
Biological Classification

• identification and classification of organisms; a component of systematics

• to arrange organisms in categories that reflect phylogeny

Systematics

Phylogeny
Biological Classification

• concerned with the diversity of life and reconstruction of phylogenetic histories

• to classify species based on evolutionary affinities

Phylogeny

Phylogeny
Biological Classification

– a representation of the hypothetical evolutionary history of a group of organisms

Phylogenetic analysis

Phylogeny
Biological Classification

– study of the genealogical relationships among species

Phylogenetic inference

Phylogeny
Biological Classification

• process of developing an estimate of the evolutionary history of a group of organisms

  • the unit of data used is the character

  • Plesiomorphic (ancestrtal)

  • Apomorphic (derived)

• Root

• Node

• Branch

• Branch length

• Clade

Parts of a Phylogenetic Tree

• _________ – the common ancestor of all taxa

• _________ – represents a taxonomic unit

• _________ – defines the relationship of the taxa in terms of descent and ancestry

• _________ – represents the number of changes that have occurred in the branch

• _________ – a group of two or more taxa that includes both their common ancestor and all their descendants

Monophyletic

Describing Groups in a Phylogenetic Tree

______________ - includes all of the descendants of a single common ancestor

Paraphyletic

Describing Groups in a Phylogenetic Tree

_______________ - includes some, but not all, of the descendants of a single common ancestor

Polyphyletic

Describing Groups in a Phylogenetic Tree

________________ - not based on common ancestry

1. Plesiomorphic

2. Apomorphic

Types of Characters

1. _____________ – primitive characteristics shared among all of the species of the cladogram and with the common ancestor

2. _____________ – derived characteristics; homologies that evolved after a branch diverged from the phylogenetic tree

Synapomorphies

______________ – shared derived states

Homoplasious characters

__________________ — shared by a set of species but not present in their common ancestor

Homoplasious characters

A homoplasy is a character shared across clades in a phylogeny that don't share direct ancestry, are an indication of inconsistency between the phylogenetic tree and the sequences used to build it.

____________________ — result from either convergent evolution or evolutionary reversal

Distance methods

Methods to create trees
(Also state the subtype of method if applicable)

________________ – based on genetic distance values

Distance methods; Neighbor-joining method

Methods to create trees
(Also state the subtype of method if applicable)

______________ – does not assume equal rates of evolution

Distance methods; UPGMA (Unweighted Pair Group Method with Arithmetic Mean)

Methods to create trees
(Also state the subtype of method if applicable)

– assumes equal rates of evolution

Maximum Parsimony

Methods to create trees
(Also state the subtype of method if applicable)

_______________ — a method of reconstructing the phylogeny by preferring the tree that produces the least number of evolutionary changes

Maximum likelihood

Methods to create trees
(Also state the subtype of method if applicable)

_______________ – calculates the probability of a data given a tree and model

Bayesian methods; Bootstrap

Methods to create trees
(Also state the subtype of method if applicable)

__________________ – propose the most likely evolutionary model given the data and known phylogenetic relationships

• *___________ – generates confidence intervals of parameter estimates