Phylogeny & Taxonomy Flashcards
w4
taxonomy
- science/study of classification
- taxonomic ranks for cellular organisms inc domain, kingdom, phylum, class, order, family, genus, sp
phylogeny
evolutionary history of groups of organisms (such as clade, sp or individuals, which may be referred to as taxa)
phylogenetics
- systematic study of organism relationships based on evolutionary similarities & diffs
- modern taxonomy based on phylogeny
tree of life
- 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
phylogenetic tree
- hypothesis of genealogical relationships…
- inferred from observed traits (“characters”)
basic assumptions of phylogenetic tree
- organisms are related by descent from common ancestor
- characteristics change over time as organisms evolve
- new clades created by binary splitting
clade encompassing a group of taxa
- consists of last common ancestor (taxon) of those taxa…
- and all taxa that descended from last common ancestor
importance of phylogenetics
- 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
character
heritable feature of organism
e.g…
no. of appendages?
feathers present?
no. of teeth?
character states
values character can take
eg. 1, present
0, absent
2 important types of characters used for reconstructing phylogenies…
- molecular characters -> inc. seqs of DNA, RNA, genome, protein
- morphological characters -> inc. structures, behaviours, lifestyles
internal node
hypothetical ancestor of 2 given taxa
root node
hypothetical common ancestor of all taxa in tree
branches
accumulation of evolutionary change through time
tip
a taxon (sp, family, order etc.)
sister taxa
taxa closer to each other than any others on the tree
outgroup
most distantly related taxon to all the others
(the others can be referred to as the ingroup)
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?
no -> observed similarities can come from 2 sources…
- similar characters could have been inherited from common ancestor (homology)
- OR…
- could have evolved independently (homoplasy)
homology
- similarity between structures in diff organisms…
- that is attributable to their inheritance from common ancestor
homoplasy
- similar traits in diff organisms…
- that do not share common ancestor but due to convergent evolution
So the 2 taxa that share largest no. of homologies are the closest relatives, right?
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
apomorphy
- derived character state that has evolved within a taxa
- can be used to separate one taxa from other
synapomorphy
apomorphy shared by 2+ taxa and their most recent common ancestor
plesiomorphy
- primitive / ancestral character state…
- that is homologous within particular group of organisms
- but is not unique to members of that group
symplesiomorphy
plesiomorphy shared by 2+ taxa of a group
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
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
Hennig’s 2 key principles of cladistics
-
only features that are informative about phylogenetic relationships are shared, derived homologies
-> rules out both homoplasies & plesiomorphies/symplesiomorphies of taxa being studied - proper classification of organisms requires grouping taxa into clades / monophyletic groups
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)
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)
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)
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
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
cambrian lobopodiums
- group of extinct organisms
- close affinities to living anthropods
- long bodies
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
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
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
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
crown & stem group
Any clade can theoretically be ÷ into 2 components:
- crown group: contains living taxa of group & most recent common ancestor & all of its descendants (both extant & extinct)
- 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
