Lecture 2: The Tree of Life and Biodiversity [G] Flashcards
Wednesday 2nd October 2024
When did Darwin first sketch his tree of life?
In 1837
What was La Scala Nature?
- A view from the Medieval era (500-1500 AD) that was the hierarchal model of life arranged as the staircase to heaven.
- Example: Minerals → Fire → Plants → Animals → Humans → Angels → God.
- The higher the being is in the chain, the more attributes it has, including all the attributes of the beings below it.
How did Darwin come to his conclusion over the tree of life?
- Realised that fossils of animals no longer existed.
- Realised that there were the same number of organisms on earth
- Realised that some organisms disappeared and were subsequently replaced by other forms.
When did Darwin publish ‘On the origin of species’?
In 1859. This book first formalised the idea of natural selection driving evolution.
What happens to lineages over time?
They change and diverge
In Medieval times, what was used to show the hierarchy of organisms?
The Great Chain of Being
When did Linnaeus draw his tree of Classification?
In 1735
Who made the first attempt at systematic classification?
Linnaeus
How did Linnaeus’ tree of classification work?
He put the best species at the top, and organisms that we eat at the bottom. ( we were at the top)
Who introduced binomial nomenclature for systematic classification?
Linnaeus
Although Linnaeus did introduce binomial nomenclature for systematic classification, what was still wrong with his classification system?
Retained medieval biases (e.g., misclassification of whales as fish).
Which levels of classifiaction were used by Linnaeus?
Kingdom, Class, Order, Family, Genus, Species. (Modern taxonomy includes additional categories like domain and phylum, which Linnaeus did not have, but his work laid the groundwork for future developments in biological classification.)
Kings Play Chess on Fancy Gold Squares
Kingdom Phylum Class Order Family Genus Species
Was the medieval ‘march to progress’ correct or incorrect?
Incorrect
Describe Darwin’s insights from 1837
- Darwin conceptualized the idea that all living organisms are connected through a “Tree of Life.” nstead of viewing life as a hierarchical ladder (common in medieval thinking), he proposed that life forms diverged from common ancestors in a branching pattern. Each branch represented a lineage, and the points where branches split (nodes) represented shared ancestors.
- Recognized species extinction and replacement, but lacked knowledge of genetic mechanisms.
- In 1837, Darwin sketched his first evolutionary tree in his notebooks, marking it with the phrase “I think” at the top. This sketch demonstrated his realization that species are linked through shared ancestry and that this connection can be depicted as a tree with diverging branches.
- While Darwin understood the “what” of evolution — that species evolve and are connected through shared ancestry — he did not yet understand the “how.” At this time, the mechanisms of heredity and genetic variation were unknown. These would only be clarified later through Gregor Mendel’s work on inheritance and the eventual discovery of DNA.
What did Darwin do in the ‘Origin of Species’ 1859?
He first formalised the idea of natural selection driving evolution.
What eventually bridged the gap between Darwinian theory and modern genetics?
Gregor Mendel’s genetic experiments with peas
In 1937, who redefined evolution?
Theodosius Dobzhansky
When did Theodosius Dobzhansky redefine evolution?
In 1937
What did Theodosius Dobzhansky redefine evolution as in 1937?
‘a change in allele frequency in a gene pool’.
Is it true that Edward Hitchock used fossil evidence and branching diagrams (tree) to expand on Darwin’s findings?
Yes
Do mutations/variation cause divergence?
Yes. This is what Darwin predicted. He just did not have the experimental evidence to back this up.
What experiment was used in this experiment to investigate antibiotic resistance?
‘Bacteria exposed to increasing antibiotic concentrations evolved resistance in just 11 days. This showed that sucessive e mutations enable survival and adaptation under environmental pressures.’ Proved darwin’s idea that mutations can cause divergence.
How can linneages be examined?
- Behavioural and ecological studeies
- Molecular evidence (DNA, RNA, proteins)
- Morphological traits (both living and fossil species)
What evidence can be used to investigate the evolution of living and fossil whales?
- Morphological traits like how they feed, and teeth
- Molecular (the best evidence)
- Fossil records
Homologous Traits and Apomorphies
Key Definitions:
Homologous Traits: Derived from a common ancestor.
Apomorphy: A derived trait unique to a taxonomic group.
Synapomorphy: A shared derived character among multiple groups.
Homologous Traits and Apomorphies
Key Definitions:
Homologous Traits: Derived from a common ancestor.
Apomorphy: A derived trait unique to a taxonomic group.
Synapomorphy: A shared derived character among multiple groups.
What are Cetaceans?
Marine mammals that include whales, dolphins, and porpoises
How many suborders of whale are there?
2
How many years ago did the 2 suborders of whale diverge from each other?
34 million years ago
What are the 2 suborders of whale called?
- Mysticetes (baleen whales)
- Odontocetes (toothed whales)
Describe Mysticetes whales
- Baleen whales have baleen plates instead of teeth to filter food from the water.
- They are generally larger than toothed whales, and include the blue whale, humpback whale, and right whale.
Describe Odontocetes whales
Also known as toothed whales, they use teeth to hunt for prey, and include orcas, sperm whales, dolphins, and porpoises.
Are all features of morphology used in classification?
No, as some features of morphology are of no use in classification. This is because some features might be misleading due to convergent evolution or evolutionary loss.
Why is morphology often combined with molecular data (DNA and proteins) ?
To ensure more accurate classifications. Molecular evidence can help resolve ambiguities when morphological traits alone are insufficient.
How are whales classified as mammals? (homologous traits)
- By having a placenta
- By producing milk
- By having hair follicles
What are useful for phylogeny?
- Homologous traits (also called derived traits or apomorphies
What is a Homology?
Any similarity of traits between organisms because of shared ancestory. Not due to inheritance
What are some homologies of mammals?
- Having a placenta
- Producing milk
- Having hair follicles
Are fins and hands homologous?
Yes, due to divergent evolution.
What is divergent evolution?
Divergent evolution is a process where two or more species or groups evolve from a common ancestor and gradually develop different traits or features due to adaptation to different environments, lifestyles, or ecological niches.
What process causes the webbing between the digits of hands to disappear?
Apoptosis
How are fins made?
Due to a change in developmental programming
What is a Synapomorphy?
An apomorphy shared by 2 or more taxa/ derived form or trait shared by 2 or more taxa
Derived traits can be…
reduced or lost
What is the difference between derived and ancestral traits?
- Ancestral traits are traits that were present in a common ancestor of a group of organisms. These traits can be morphological, physiological, behavioural or molecular.
- Derived traits are features that evolve in a species or lineage due to mutation in a more recent ancestor.
What happens to the hind limb in dolphin embryos?
- It develops, but it is then reabsorbed.
- However, it can be seen if the skin of the dolphin is taken off.
What were the features of the whale that existed 40 million years ago?
- Reduced hind limbs
- Inflexible elbow, like modern whales
- Heterodont, with interlocking teeth
- Tympanic bulla (part of the ear), with a thickened involucrum. (found in tympanic bulla) ( enabled better underwater hearing.
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What does a tympanic bulla allow whales to do?
Allows whales to hear sound underwater
What is one difference between whales from 40 million years ago and whales today?
Whales from 40 million years ago had more complex teeth at the back of their mouths. This was called Heterodont Dentition.
How long ago did ancient whale Dorudon live?
Around 40mill years ago. Had many of the above ancient whale features
What was Pakicetus?
A whale that existed 50 million years ago, and had legs
In simple terms, what is a double pulley astragulus?
An ankle bone
Is it true that a double pulley astragulus (ankle bone) is a synapomorphy among artiodactyls?
yes
What is a synapomorphy among cetaceans?
An involucrum (thickened) that allows organisms to hear underwater.
What is an artiodactyl?
a mammal that has an even number of functional toes on each foot.
Why should morphology be supplemented with molecular data?
Because molecular data is the best possible evidence
What does molecular evidence include?
- protein sequences of casein and cytochrome b
- 26 genetic loci DNA sequences
- transposon (jumping gene) positions
What is the closest living relative to a whale?
A hippo
What is cladistics?
classification where organisms are grouped by most recent common ancestry. It focuses on grouping species into clades, which are groups that include a common ancestor and all its descendants.
What does a node represent in a phylogenetic tree?
A common ancestor. Shows the point of divergence and so where lineages split.
How should a phylogeny tree be read?
From its nodes, not the terminal branches
What is a clade?
An ancestor and all of its descendants (identified by cutting the tree at a single point (monophyletic groups)).
What is Monophyly?
a clade that comprises of an ancestor and all its descendants.
What is Paraphyly?
an ancestor and some but not all its descendants.
In cladistics, when is the only case where a taxonomic unit is legitimate ?
only when it is a monophyletic group. This means the group must include: A single common ancestor, and all of its descedants.
What is an autapomorphy?
self-derived character.
A derived trait that is unique to a given taxon.
Do autapomorphies provide useful grouping information?
No, because it is a derived trait that is unique to a given taxon.
Describe 2 autapomorphies of platypuses
- They lay eggs
- They have venom glands connected to hollow spurs on their hind legs
What are the 3 domains of life?
Bacteria, archea, eukarya
What are the 3 domains of life based upon?
They are based upon the sharing of genes by horizontal gene transfer (HGT)
Who said that ‘Nothing in biology makes sense except in the light of evolution’?
Theodosius Dobzhansky
How many metres long was the Dorudon?
5 metres long
READ A PHLOGENETIC TREE FROM THE NODES, NOT THE TAXA
READ A PHYLOGENETIC TREE FROM THE NODES, NOT THE TAXA
Think of a node as a swivel joint, not as a fixed weld
Think of a node as a swivel joint, not as a fixed weld
In cladistics, a taxonomic unit is legitimate only when monophyletic.
In cladistics, a taxonomic unit is legitimate only when monophyletic.
Why don’t autapomorphies provide useful grouping information?
Because they unique to a single taxon, and are not shared by any other taxa.
In cladistics, what is the primary evidence used to determine evolutionary relationships and construct phylogenetic trees?
synapomorphies because they directly reflect shared evolutionary history. By focusing on synapomorphies, cladistics avoids misinterpretations caused by convergent evolution or ancestral traits.
What is used for molecular evidence in phylogeny?
26 genes and specific proteins (e.g., cytochrome b) used to refine evolutionary relationships.
What are some modern classfication challenges?
Advances in molecular biology have shifted classification paradigms. Complex relationships between domains of life (e.g., horizontal gene transfer) challenge traditional methods.
1) What misconception did Linnaeus have about whales in his classification system?
Linnaeus incorrectly classified whales as “fish” rather than mammals. This mistake stemmed from his reliance on superficial physical traits like streamlined bodies and fins, which resemble fish more than typical mammals, rather than considering deeper features like placentas, milk production, or the presence of hair follicles that classify them as mammals.
2) What organism did Linnaeus incorrectly classify as the “top fish”?
Linnaeus considered marine mammals such as dolphins, sperm whales, baleen whales, and even the manatee to be the “top fish” in his classification. This error arose because he grouped organisms based on their aquatic habitats and outward appearances rather than their evolutionary and biological traits.
