1. http://www.youtube.com/watch?v=GxCRr1uV2I8 From BBC Life of Birds
Jargon
From BBC Life of Birds
Brian O’Meara
EEB464 Fall 2017

2. Learning objectives
Precise language is essential to science Learn and discuss particular vocabulary useful in rest of semester

3. What is a species?

4. After Coyne and Orr. Speciation. (2004). Table 1.1, p. 27
Biological
Species are groups of interbreeding natural populations that are reproductively isolated from other such groups (Mayr 1995) B
Genotypic cluster
A species is a [morphologically or genetically] distinguishable group of organisms that has few or no intermediates when in contact with other such clusters (Mallet 1995) C
Recognition
A species is that most inclusive population of individual biparental organisms which shares a common fertilization system (Patterson 1985) D
Cohesion
A species is the most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms (Templeton 1989) E
Ecological
A species is a lineage (or a closely related set of lineages) which occupies an adaptive zone minimally different from that of any other lineage in its range and which evolves separately from all lineages outside its range (Van Valen 1976) F
Evolutionary
A species is a single lineage of ancestral descendant populations or organisms which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate (Wiley 1978, modified from Simpson, 1961) G
Phylogenetic 1
A phylogenetic species is an irreducible (basal) cluster of organisms that is diagnosably distinct from other such clusters, and within which there is a paternal pattern of ancestry and descent (Cracraft 1989) H
Phylogenetic 2
A species is the smallest [exclusive] monophyletic group of common ancestry (de Queiroz and Donoghue 1989) I
Genealogical
A species is a basal, exclusive group of organisms all of whose genes coalesce more recently with each other than with those of any organisms outside the group, and that contains no exclusive group within it (Baum and Donoghue 1995; Shaw 1998)
Two points, any question
After Coyne and Orr. Speciation. (2004). Table 1.1, p. 27

5. Speciation
Allopatric
Parapatric
Sympatric

6. Willi Hennig, Phylogenetic Systematics, 1966. p. 19

7. Willi Hennig, Phylogenetic Systematics, 1966. p. 71
This history of splitting creates a series of nestings. We typically show this as a tree, but other ways of showing this nesting are possible.
Willi Hennig, Phylogenetic Systematics, p. 71

8. Tree = phylogeny = cladogram (if no branch lengths) = connected graph with no cycles

9. Taxon = OTU (operational taxon unit) = Leaf = Terminal = Terminal Node

10. Taxon = OTU (operational taxon unit) = Leaf = Terminal = Terminal Node
Taxa are often extant (living) organisms, but they need not be. Fossils can be taxa, viruses sampled at different times, etc. and so not all taxa need occur at the same time.

11. Branch = edge

12. Branch = edge
May have length, which may correspond to time, amount of character change, probability of character change, etc.

13. [Internal] Node

14. [Internal] Node
Where different edges meet. If all have just two descendant branches, tree is “bifurcating” or “fully-resolved” or “dichotomous”. Nodes with more branches are “polytomies” or “multichotomies”

15. Root [node]

16. A rooted tree (most common) has a node that represents the most recent common ancestor (MRCA, or LCA (least common ancestor)) of all the taxa. A rooted tree (directed graph) shows the direction of time.
Root [node]

17. Clade: ancestor and all its descendants (a “monophyletic” group”)

18. Paraphyletic group: ancestor and some but not all its descendants

19. Polyphyletic group: even worse
In practice, you can’t really tell paraphyletic from polyphyletic from just a set of taxa (rule of thumb: if the group of taxa is a clade except a few subclades (maybe just one) are missing, it’s “paraphyletic”; if a lot of things are missing, it’s “polyphyletic”). You can tell if branches are included in the definition (ancestor included or not -> para vs poly). But basically, monophyletic groupings good, others bad (in terms of being “natural groups”)
Polyphyletic group: even worse

20. We often learn taxonomic ranks (Kingdom, Phylum, Class, Order,. )
We often learn taxonomic ranks (Kingdom, Phylum, Class, Order,...). Almost all systematists now only give names to clades (which has caused some major changes: goodbye, dicots (“angiosperms that aren’t monocots”)). However, there has been a trend to drop the ranks from taxonomy. Arguments in favor are that rank is arbitrary (see animation), has no useful information (what does it tell you that mammals are a class but beetles are an order?), and can be misused (as when people compare genera without taking the phylogeny into account, or compare number of families in the tropic and temperate zones -- see Darrin Hulsey’s lectures). There’s even a new taxonomic system, Phylocode, which aims to establish a taxonomy naming only clades and avoiding rank. Arguments in favor of using rank are that it makes learning easier (so everyone learns the same plant families) and that it contains the information that two groups of equal rank must be non-overlapping in membership. Rank in taxonomy was a hot issue several years ago, but it seems to have quieted down (perhaps because there are few undecideds to fight over anymore). For what it’s worth, I personally favor rank-free taxonomy (though I still believe in the species rank, unlike some).
Genus?

21. If you can’t compare genera, what can you compare
If you can’t compare genera, what can you compare? Sister groups: a pair of clades descending from the same node. They’ve had the same time to evolve and started from the same ancestor. You’ll learn other ways to make phylogenetically-correct comparisons with Darrin. But just remember to think of species, genera, or any other group like people in a small town. If half of them have blue eyes, it might be due to inheritance from a blue-eyed ancestor, rather than some adaptive significance of blue eyes in that town. You must take relationships into account.

22. Taxa sister to the focal group (and sometimes taxa sister to the focal group and its closest relative) are sometimes called “outgroups”. They help root the tree (show you which way is down)

23. Brady S. G. , T. R. Schultz, B. L. Fisher, and P. S. Ward. 2006
Brady S.G., T. R. Schultz, B.L. Fisher, and P.S. Ward “Evaluating alternative hypotheses for the early evolution and diversification of ants” PNAS 103:

24. Characters
Homology: Similarity due to shared ancestry (i.e., humans, birds, and turtles all having four limbs)
Homoplasy: Similarity, but not due to shared ancestry (i.e., convergence of dolphins and ichthyosaurs on similar shape)

25. Ex: Sharks living in water (compared to tetrapods living on land)
Characters
Plesiomorphy: An ancestral (“primitive”) character state (with reference to another, derived, state)
Symplesiomorphy: Plesiomorphy shared by ≥ 2 taxa
Apomorphy: A derived (“advanced”) character state (with reference to another, ancestral, state)
Synapomorphy: Apomorphy shared by ≥ 2 taxa
Autapomorphy: Apomorphy possessed by one taxon
Ex: Sharks living in water (compared to tetrapods living on land)
Ex: Whales living in water (compared to other tetrapods living on land)
Definitions from Futuyma, Evolutionary Biology, 1998

26. Characters Note correct plural!
Plesiomorphy: An ancestral (“primitive”) character state (with reference to another, derived, state)
Symplesiomorphy: Plesiomorphy shared by ≥ 2 taxa
Apomorphy: A derived (“advanced”) character state (with reference to another, ancestral, state)
Synapomorphy: Apomorphy shared by ≥ 2 taxa
Autapomorphy: Apomorphy possessed by one taxon
Note correct plural!
Definitions from Futuyma, Evolutionary Biology, 1998

27. Wings have been exapted for shading
From BBC Life of Birds
GOULD and VRBA. EXAPTATION - A MISSING TERM IN THE SCIENCE OF FORM. Paleobiology (1982) vol. 8 (1) pp. 4-15

28. Advanced and primitive
Another aspect of traditional education: progress in evolution from simple, “primitive” organisms to “advanced” ones (oddly, often represented by humans).
© Micheletb (Wikimedia Commons contributor)

29. Advanced and primitive
Icons ©Wellcome Trust

30. Advanced and primitive
Icons ©Wellcome Trust

31. Advanced and primitive
Position on the tree alone does not tell you about “primitive” or “advanced” taxa -- in two different but both valid trees, humans appear at completely different positions. Pruning, whether by extinction or just by not including certain taxa on a tree, can make the tree have a particular form, but all extant organisms are tips on the tree and have had the same amount of evolutionary time from the root of the tree (also called their most recent common ancestor, or MRCA). Some have had more shared time together than others. And they often are a mixture of new and ancient traits. Some taxa may more closely resemble hypothetical ancestors than others, but they are not ancestral to other extant taxa, and just position on the tree cannot tell you how similar they are to their ancestors. Just the same, people often make this mistake.
Icons ©Wellcome Trust