Phylogenetic Tree)

Biol 317: Plant Classification & Identification Summer 2011

Instructor: Valerie Soza Office: 408 Hitchcock Office hours: by appointment Email: [email protected] Course website: http://courses.washington.edu/bot113/summer/2011 TA: Pat Lu-Irving

Peer TAs: Willie Foster, Shula Harkavy, Michelle Mark Handouts

Course information sheet

Syllabus

Reading assignments online

Medicinal Herb Garden project

Lab exercises for this week available in lab Nomenclature

Why naming is important? George

http://popular-cartoon.blogspot.com/2011/02/george-of-jungle.html Nomenclature

Why naming is important? George George Bush

http://en.wikipedia.org/wiki/George_H._W._Bush Nomenclature

Why naming is important? George George Bush George W. Bush George W. Bush, Jr.

http://en.wikipedia.org/wiki/George_W._Bush Nomenclature

Problems with common names No rules for usage! One kind of plant will have many different common names. The same common name may be associated with many different plant species.

“potato” = Solanum tuberosum, Dioscorea bulbifera, Apios americana, Dioscorea batatas, Solanopteris bifrons, Plectranthus rotundifolius, Allium cepa, Gastrodia sesamoides, Ipomoea batatas, Solanum macranthum, Ipomoea pandurata, Solanum jasminoides, Dioscorea esculenta (Mabberley 1997) http://tombutton.users.btopenworld.com/potato_1.jpg Early Attempts at Formal Nomenclature

1700s: Very specific, descriptive names Up to a dozen Latin adjectives

Example: http://en.wikipedia.org/wiki/Rosa_canina Early scientific names for the common wild briar rose Rosa sylvestris inodora seu canina (“odorless woodland dog rose”) Rosa sylvestris alba cum rubore, folio glabro (“pinkish white woodland rose with hairless leaves”) Linnaeus System “Species Plantarum” (1753)

Carl von Linné or Carolus Linnaeus

Binomial nomenclature Genus + species names = scientific name e.g., Homo sapiens, Solanum tuberosum or Homo sapiens, Solanum tuberosum

Carolus Linnaeus, detail of a portrait by Alexander Roslin, 1775; in the Svenska Porträttarkivet, Stockholm. Hierarchical system

Kingdom Plantae Phylum Magnoliophyta Class Magnoliopsida Order Solanales Family Solanaceae Genus Solanum Species Solanum tuberosum L. Hierarchical system

Kingdom Plantae Phylum Magnoliophyta Class Magnoliopsida Order Solanales Family Solanaceae Genus Solanum Species Solanum tuberosum L. Flexible system

Kingdom Plantae Phylum Magnoliophyta Class Magnoliopsida Subclass Asteridae Order Solanales Family Solanaceae Subfamily Solanoideae Tribe Solaneae Genus Solanum Species Solanum tuberosum L. Subspecies S. tuberosum ssp. andigena Classification

What is Classification? The sorting of things into groups and the assigning of names to those groups. Biological science - The grouping of organisms into categories based on shared characteristics or traits.

Why is this important? Dealing with large amounts of information. Understanding and communication about the natural world. Power of prediction. To make sense of comparative studies… prevents comparing ‘apples to oranges’ Classification is the way we communicate about biological diversity! How do we classify organisms?

Group organisms based on how alike they appear…

Linnaeus’ Sexual System: Used the presence or absence and number of sexual parts as the basis for classification. -24 classes for all plants, on the basis of stamens. -Classes into orders on the basis of styles in each flower.

http://www.robinsonlibrary.com/science/natural/biography/graphics/linnaeus3.gif How do we classify organisms?

Group organisms based on how alike they appear…

Today, scientists use: 1. Visible morphology - structures 2. Anatomy – internal or microscopic structures 3. Chemicals – presence/absence, pigments, toxins, etc. 4. Genetics – chromosome, DNA similarity Linnaeus’ Classification

“Species Plantarum” (1753)

100 years before anyone had heard of the idea of evolution. At the time, people thought species were static or unchanging.

Linnaeus’ system was artificial.

Artificial classification - with no regard for evolutionary relationships. (e.g., any classification of things other than living things would have to be artificial). Natural Classification

Charles Darwin (1859 – On the Origin of Species) was the first to suggest that any classification of life should be “genealogical” and would naturally be hierarchical. Charles Darwin (1859) Haekel’s tree of life (1866)

http://universe-review.ca/I10-70-Darwin.jpg http://plus.maths.org/issue46/features/phylogenetics/Haeckel.png Systematics as a process

Since Darwin, scientists have placed more and more emphasis on developing natural classification systems that reflect the evolutionary relationships of a group of organisms.

Systematics = the study of biological diversity and its evolutionary history. Basic activities include classification and naming (taxonomy).

Just like any other kinds of science, systematics is a process. The goal to classify life based on its evolutionary history is an ongoing process.

As a result, our classifications are dynamic… Classifications are dynamic…

http://www.wpclipart.com/food/fruit/tomato/tomato.png

Before: Lycopersicon esculentum Now: Solanum lycopersicum

(Spooner et al., 1993) Phylogenetic Classification

A “good” classification system should have power of prediction.

Ever since Darwin, the goal of classification has been a “natural” classification that reflects evolutionary relationships.

Phylogeny = the pattern of evolutionary relationships among species; a branching evolutionary tree of life.

Today our goal is phylogenetic classification = a hierarchical ordering of taxa according to phylogenetic relationships consisting of a nested set of ever more inclusive groups. Phylogeny

Phylogeny is often presented as a diagram (a phylogenetic tree).

http://media-2.web.britannica.com/eb-media/98/5598-004.gif

http://www.sp.uconn.edu/~terry/DHE/Mione1.jpg Phylogenetic tree

Ingroup Outgroup Group 2 Group 1 H G F E D C B A Terminal branch Node = most recent common ancestor

Internal branch = ancestral species Root = common ancestor time Ingroup = the study group. Sister group = the group that is most closely related to the ingroup; closest outgroup. Outgroup = a more distantly related group. The “tree thinking challenge”

Sister relationships are reciprocal relationships!

(Baum et al. 2005)

Topology = pattern of branching of a phylogenetic tree. The “tree thinking challenge” cont.

(Baum et al. 2005) The “tree thinking challenge” cont.

(Baum et al. 2005) Monophyletic groups

H G F E D C B A

Monophyletic group (or clade) = a group composed of a common ancestor and all of its descendents. [mono = one, phylum = tribe] Paraphyletic groups

H G F E D C B A

Paraphyletic group = a group containing a common ancestor and some, but not all, of its descendents. [para = near, “not quite”, phylum = tribe] Polyphyletic groups

H G F E D C B A

Polyphyletic group = a group that does not include the common ancestor of its members. [poly = many, phylum = tribe] Phylogenetic classification

Phylogenetic classification = a hierarchical ordering of taxa according to phylogenetic relationships consisting of a nested set of ever more inclusive groups. Or, in a more concise way, the use of phylogeny to produce the classification taxon (plural – taxa) = any named group at any hierarchical level (could be a species, genus, family, etc.).

Goal of phylogenetic classification: recognize monophyletic groups only! In other words, identify a nested, hierarchical set of monophyletic groups. Phylogenetic classification

http://www.wpclipart.com/food/fruit/tomato/tomato.png

Before: Lycopersicon esculentum Now: Solanum lycopersicum

Phylogenetic classification has more power of prediction (Spooner et al., 1993) Phylogenetic reconstruction

Phylogenetic reconstruction (cladistics) in systematics = the process by which we determine or estimate relationships (from the present diversity to the pattern of evolutionary relationships).

It’s a hypothetical reconstruction of the sequence of evolutionary events.

Phylogenetic hypotheses are subject to further evaluation when new data become available.

BUT HOW DO WE RECONSTRUCT PHYLOGENY? Phylogenetic reconstruction

We look for comparable similarities (characters).

“The characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical.” (Charles Darwin 1859)

Character = a variable trait of an organism or group.

Character states = alternate forms of a character. Homology

Homology = similarity due to inheritance of a feature from a common ancestor. A character that arose with the evolution of a group and is shared due to common ancestry is homologous. Homologous character: wing of all birds. Non-homologous character: wing of birds, bats, and insects.

Two components of homology: When we talk about homology as evidence for relationship, we must refer both to a trait (character) and a group of organisms. Synapomorphy

Synapomorphy = shared, derived character. (from Gr. syn—together (shared) + apo—away + morph—form)

A character in two or more groups that can be traced back to the same feature in the common ancestor of those groups, and not found in other organisms.

Synapomorphies diagnose monophyletic groups.

Example: feathers on birds. Symplesiomorphy

Symplesiomorphy = shared, ancestral character. (from Gr. syn—together (shared) + plesio—near + morph—form)

An ancestral trait that is shared by two or more modern groups and can be traced back to their common ancestor, but is not found among all descendants of this ancestor.

Symplesiomorphies diagnose paraphyletic groups.

Example: keratin scales on reptiles. Convergent character

Convergent character is NOT homologous! (from Latin: con—together + vergere—to incline together)

A trait due to evolution in parallel in two different organisms, i.e., convergent evolution or parallel evolution, and not due to common ancestry.

Convergent characters diagnose polyphyletic groups.

Example: wings on birds, bats, and insects. Determining whether a character is derived or ancestral

Polarity = direction of evolutionary change.

Most commonly used method to determine polarity: Outgroup comparison = inference from distribution of character states in sister group. For a variable character with two or more states, the state occurring in the outgroup is ancestral.

Phylogenetic reconstruction = grouping species by shared derived states of characters. Phylogenetic reconstruction from characters

Parsimony = the principle that the explanation requiring the least change is preferred. Characters Taxa a b c outgrp 0 0 0 1 0 1 0 2 1 0 1 3 1 1 1

out 1 2 3 out 1 3 2 out 1 2 3 c b c b a c a c b c a a a b b

4 steps 5 steps 6 steps Sources of character data

Actual phylogenetic inferences often use many taxa and a large number of characters.

Sources of data = any comparative data. morphology cytology behavior DNA sequences etc. Inferring phylogenies using DNA sequences

Real example with DNA sequence data (nucleotide sites). Green plants

Green plants

Land plants

Bryophytes Tracheophytes (vascular plants)

Seed plants

“Green algae”

Gymnosperms Angiosperms

ycophytes

Mosses

Hornworts

Liverworts

Ferns L Conifers

(Stefanovic et al. 1998)