1
Q
taxonomy
A
- science/study of classification
- taxonomic ranks for cellular organisms inc domain, kingdom, phylum, class, order, family, genus, sp
2
Q
phylogeny
A
evolutionary history of groups of organisms (such as clade, sp or individuals, which may be referred to as taxa)
3
Q
phylogenetics
A
- systematic study of organism relationships based on evolutionary similarities & diffs
- modern taxonomy based on phylogeny
4
Q
tree of life
A
- metaphor, model & research tool used to explore evolution of life & describe relationships between organisms, both living & extinct
- graphical / diagrammatic representation of biological entities connected through common ancestors
5
Q
phylogenetic tree
A
- hypothesis of genealogical relationships…
- inferred from observed traits (“characters”)
6
Q
basic assumptions of phylogenetic tree
A
- organisms are related by descent from common ancestor
- characteristics change over time as organisms evolve
- new clades created by binary splitting
7
Q
clade encompassing a group of taxa
A
- consists of last common ancestor (taxon) of those taxa…
- and all taxa that descended from last common ancestor
8
Q
importance of phylogenetics
A
- establishing relationships of organisms
- permitting more precise approach to studying “biodiversity” & to build classification of organisms
- reconstructing evolutionary histories & processes
- developing better evolutionary models & enabling predicting power
9
Q
character
A
heritable feature of organism
e.g…
no. of appendages?
feathers present?
no. of teeth?
10
Q
character states
A
values character can take
eg. 1, present
0, absent
11
Q
2 important types of characters used for reconstructing phylogenies…
A
- molecular characters -> inc. seqs of DNA, RNA, genome, protein
- morphological characters -> inc. structures, behaviours, lifestyles
12
Q
internal node
A
hypothetical ancestor of 2 given taxa
13
Q
root node
A
hypothetical common ancestor of all taxa in tree
14
Q
branches
A
accumulation of evolutionary change through time
15
Q
tip
A
a taxon (sp, family, order etc.)
16
Q
sister taxa
A
taxa closer to each other than any others on the tree
17
Q
outgroup
A
most distantly related taxon to all the others
(the others can be referred to as the ingroup)
18
Q
using phenetics school of thought…
given a group of taxa, can we be confident that the 2 taxa that are most similar overall are the most closely related?
A
no -> observed similarities can come from 2 sources…
- similar characters could have been inherited from common ancestor (homology)
- OR…
- could have evolved independently (homoplasy)
19
Q
homology
A
- similarity between structures in diff organisms…
- that is attributable to their inheritance from common ancestor
20
Q
homoplasy
A
- similar traits in diff organisms…
- that do not share common ancestor but due to convergent evolution
21
Q
So the 2 taxa that share largest no. of homologies are the closest relatives, right?
A
no.
- all homologies are not equal
- some homologous characters were recently derived, others are ancient features of a lineage
- only shared, derived features (synapomorphies) are informative about close relationships
22
Q
apomorphy
A
- derived character state that has evolved within a taxa
- can be used to separate one taxa from other
23
Q
synapomorphy
A
apomorphy shared by 2+ taxa and their most recent common ancestor
24
Q
plesiomorphy
A
- primitive / ancestral character state…
- that is homologous within particular group of organisms
- but is not unique to members of that group
25
symplesiomorphy
**plesiomorphy shared by 2+ taxa** of a group
26
**cladistics**
aka
"phylogenetic systematics"
- introduced by German entomologist Willi Hennig (1966) as **method used in phylogenetic analysis**...
- although now sometimes used to refer to the whole field
27
cladogram
- outcome of cladistic analysis: **dichotomous branching diagram** that represents a hypothesis of phylogenetic relationships
- taxa grouped into nested hierarchy defined by sharing common ancestor
28
Hennig's 2 key principles of cladistics
1. **only** features that are informative about phylogenetic relationships are **shared, derived homologies**
-> rules out both homoplasies & plesiomorphies/symplesiomorphies of taxa being studied
2. proper classification of organisms requires **grouping taxa into clades / monophyletic groups**
29
monophyletic group
- group of taxa composed only of **common ancestor** & **all its descendants**
- monophyletic group = a **clade**
- monophyletic groups characterised by **shared derived characteristics inherited from their common ancestor (synapomorphies)**
30
Paraphyletic group
- group of taxa that include most recent common ancestor, but **not all of its descendants**
- paraphyletic and polyphyletic groups **cannot be called true clades** (they don't represent full phylogenetic story)
31
polyphyletic group
- group of taxa that **does not inc common ancestor** of **all** members of group
- paraphyletic and polyphyletic groups **cannot be called true clades** (they don't represent full phylogenetic story)
32
Importance of Phylogenetics in Fossil Studies
Allow palaeontologists to use a more objective analytical method to:
- **establish evolutionary relationships** among fossil taxa and between fossil and living taxa
- precisely study "**biodiversity**" in the past and build a **classification** of fossil organisms
- integrate fossil taxa with living taxa to **reconstruct evolutionary histories and process**
- develop **better models for macroevolution**
33
eg. of how palaeontologists **use phylogenetics** to solve scientific q's
enigmatic worm = ***Facivermis yunnanicus* Hou & Chen, 1989**
- greatly elongated & limbless portion of trunk
- pear-shaped terminal swelling with 2/3 rings of hooks
- reminds us of *Luoishania longicruris*
- phylogenetic analyses **(parsimony, Bayesian inference & max. likelihood)** => ppl thinking they are more closely related to 'velvet worms'...
- indicates that *Facivermis* **lost some features over time to fit tube-dwelling lifestyle** = **rare eg. of 2ndary loss of morphological characters so early in history**
34
cambrian lobopodiums
- group of extinct organisms
- close affinities to living anthropods
- long bodies
35
importance of fossils in phylogenetics
- fossils provide **direct evidence of evolutionary history**
- contain info about evolution we **cannot obtain from living organisms** (ancient time, extinct phenotypes)
- unique morphological comboss can reveal **crucial evolutionary links** between extant taxa & fill gaps in our knowledge of **trait acquisition along lineages**
- can be used to **test phylogenetic hypothesis**
- useful in assessing direction of character evolution & could aid in detecting instances of **convergence**
- can improve **phylogenetic analyses of morphological characters**
36
evolutionary link to crocodiles & birds
- are each others closest living relatives
- phylogenetics shows birds evolved from **theropod dinosaurs** during Jurassic (around 165-150 mya)
- birds' classic small, lightweight, feathered, & winged body plan was pieced together gradually over 10s of millions of years of evolution rather than in 1 burst
37
fossils help in molecular dating
- **molecular clock**: rate of evolution at molecular level is ~ constant through time & among sp, so its possible to use molecular seqs to **estimate time when 2+ life forms diverged**
- fossils provide **min. age time constraints** for divergences of groups
- fossil calibrations are utmost source of info for **resolving distances between molecular seqs into estimates of absolute times & absolute rates** in molecular clock dating analysis
38
fossils can help us test hypotheses.
give an eg.
- *Dannychaeta tucolus* Chen et al. 2020
- Annelids are diverse group of animals (inc. earthworms, ambush predators, & suspension feeders). Figuring out their early evolution has been tricky because **genetic studies & fossils don't always match up**.
- fossils from Cambrian period show **annelids living near ocean floor**, while genetic studies suggest they might have **lived in different ways**
- scientists found new fossil (*Dannychaeta tucolus*) from Cambrian period -> type of **bristle worm** & preserved in thin tubes made of organic material
- *Dannychaeta* has **distinct head with spade-shaped parts & long side pieces**
- elongated abdomen with biramous parapodia with parapodial lamellae
- ^ this combo of features is **similar to modern Magelonidae worms**
- by studying *Dannychaeta*, scientists learned that it's **1 of oldest types of bristle worms** we know about...
- & it helps us **understand how annelids evolved over time**
- P.S. *Dannychaeta* in clade **Palaeoannelida**
39
crown & stem group
Any clade can theoretically be ÷ into 2 components:
1. *crown group*: contains **living taxa** of group & **most recent common ancestor** & all of its **descendants** (both **extant & extinct**)
2. *stem group*: **paraphyletic assemblage** composed of **fossils** that are **closer to crown group** than to any other **living** organisms
-> crown + stem = total group
-> in tree analogy, total group is crown group & all branches back to (but not including) the split with closest branch to have living members
