The Science of Systematics

  Systematics—science of biological diversity

o   Infuses evolution with taxonomy (explains why they are different)

·      Taxonomy—process of identification and classification of living or extinct organisms

·      Systematics made taxonomy more “evolutionary-accurate”

·      Idenitifcation vs. classifcation

o   Identification—individual organism process; recognizing the distinguishing characteristics that allow the correct application of a scientific name

o   Classification—multiple organisms; hierarchical arrangement of organisms having common characters

·      Embryophytes—the land plants

o   Includes non-vascular and vascular

§  Non-vascular

·      Liverworts

·      Mosses

·      Hornworts

§  Vascular

·      Tracheophytes

o   4 groups

§  Lycophytes

§  Monilophytes

§  Gymnosperms

§  Angiosperms 

                          Vascular tissues

o   Xylem—conduct H20 from roots to leaves

§  Tracheids: tube-like xylem, can branch

·      Holes—allow for pore system, adaptive in case one gets damaged

o   Phloem—conducts sugars from leaves to roots 

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·      CDE is a monophyletic group, common ancestor at X, and can “separate” fine from rest of phylogeny

·      A,C,D,E, is a paraphyletic group: violates one of the two monophyletic group rules (in this case, not all descendents are included in group)

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·      Sister groups descend from the same node (where two or more branches intersect)

·      D’s sister group is E

·      A’s sister group is B,C, D, and E

·      Nodes can rotate, but sister group still remains the same. 

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·      5-kingdom method: very inaccurate (~30 kingdoms actually)

·      artificial classification: utilitarian (practical, but simple) e.g. in field guides, not scientific

·      phenetic classification system: based on overall similarity. Looks at a lot of different characters than artificial systems. Does not account for convergent evolution (developed similar traits because of similar environment) e.g. of convergent evolution: whales + fish, old man cactus vs. pseudocactus

·      phylogenetic system: incorporates evolution into the classification system, uses the methodology of cladistics—divides characters in 3 different classes:

o   autopomorphy—derived (modified from ancestral trait) trait, restricted to single taxon

o   synapomoprphy—derived trait, shared by two or more taxa

o   plesiomorphy—ancestral trait, has not changed from condition of common ancestor (e.g. DNA, or cells in humans)

·      Precambrian           

o   Hadean

o   Archean

o   Proteozoic

o   Cambrian

o   Ordovician (non vascular plant)

o   Silvrian 250 (late Silurian = vascular)

o   Devonian diversification of vascular land plants (lycohphytes, monilophytes, seed plants)

o   Carboniferous (lycophytes)

o   Jurassic and cretaceous (flowering plants ~ 65 mya)

o   Clubmoss family (but not moss)

o   Cosmopolitan

o   Solitary sporangia in leaf axils, dehisce by a transverse slit

o   Homosporous—meiosis produces 1 size of spore 

o   Spikemoss family (still not a moss)

o   Mainly tropical

o   Strobili (strobilus: reproductive part, like cone, but not woody) are 4-sided

o   Microphylls small ~0.5-1.0 cm, often 4-ranked and dimorphic (with two sizes)

o   Heterosporous—two sizes of spores

§  Male microspores—many, smaller

§  Female megaspores—a lot, larger

o   Spiky part contains sporangia, reproductive

o   E.g. resurrection plant

o   Quillwort family

o   Cosmopolitan

o   Aquatic or moist terrestrial environments

o   Grass-like, but not grass

o   Sporangia at base of leaf

o   Heterospores (microspores, mega-spores)

o   Microphylls are very long

o   Geese and ducks may have role in spreading spores 

§  3 extant families

§  many extinct groups in fossil record

§  Carboniferous period marks height of diversity

§  Then large, woody plants (now small, herbaceous)

§  Responsible for major coal deposits 

·      Microphylls—leaves with a single, unbranched strand of vascular tissue

·      Reniform sporangia—sack where spore are produced (occur in same place as axilary buds, in axils of lvs); kidney shaped

§  Megaphylls—leaf with branched vascular strands

§  30Kb inversion in chloroplast DNA—circular DNA, usually mutation, good evolutionary marker 

o   Adder’s tongue ferns

o   Cosmopolitan

o   Leaf divided into fertile and sterile segments (good recognition feature)

o   Ophioglossum petiolatum is Top 40

o   Only above ground part we see is leaf

o   Whisk fern

o   Tropical/warm temperate

o   Roots absent, leaves reduced (good recognition feature)

o   Sporangia fused (good recognition feature)

o   E.g. Psilotum nudum

o   Horsetail family

o   Cosmopolitan

o   Wet areas

o   Whorled leaves, fused at base, jointed node

o   Strobulus at top

o   E.g. Equisetum hymale

o   Water-clover family

o   Nearly cosmopolitan

o   Wet areas

o   Sporocarp—furry bean, highly modified leptosporangia

o   Heterosporous

o   E.g. Marsilea quadrifolia

·      leptosporangia—small, thin-walled, much more effective, has annulus that is sensitive to humidity (low humidity, dries out and contracts and throws out spores. Low humidity is good because it allows conditions to keep spores airborne)

·      eusporangia—ancestral condition, large, thick-walled, thousands of spores

§  Heterospory—individual evolution; also seen in the lycophyts and monilophytes

§  Secondary growth—increase girth of a plant; produces woody tissues

§  Pollen—very mobile, pollen grian is technically a reduced male gametophyte. Effective means of sperm dispersal.

§  Seeds

o   Oldest within gymnosperms

o   Date back to the late

o   Carboniferous-early Permian

o   Monophyletic

o   tropical to warm temperate:mostly southern US

o   dioecious – “two houses” the sees are on separate inviduals (separate male and female plants)

o   Cycas revoluta and Zamia furfuracea are Top 40

o   characterized by:

§   cycasins: poisonous compounds, mostly concentrated in seeds (autapomorphy)

§   cataphylls: protective scale-like leaves (autapomorphy)

§  coralloid roots: roots modified to house cyanobacteria for nitrogen fixation (allows cycads to grow in poor soils) also an autpomorphy

§   insect pollination: usually with beetles, they grew on cones and transfer pollen

o   Dates back to late Triassic

o   Monophyletic

o   Remote areas of China

o   Dioecious

o   Ginkgo biloba is used in herbal medicine

o   Characterized by

§  Fan-shaped leaves (autap.)

§  Dichotomous venation(autap.)

§  Paired ovules(autap.)

§  Wind pollination

§  Deciduous (loose leaves in fall) (autap.)

§  Seeds often paired

§  Fleshy seed coat gives off smell 

o   Dates to Carboniferous

o   Monophyletic?

o   Cosmpolitan

o   Monoecious/dioecious (mixture; monoecious: both males and female structures on same plant)

o   Characterized by

§  Cones or modified cones

§  Often needle-like or scale-like leaves

§  Wind pollinated

o   Monophyletic

o   Temperate/tropical

o   Monoecious/dioecious

o   Each group distinctive morphologically

§  Vessels (large conducting cells in the xylem; 100x the size of tracheids; much more efficient water conductor) in wood

§  Double fertilization

§  Wind/insect pollination

§  2 single leaves that just continue to grow; have a large taproot

o   Intensive—ideal, sampling of almost all taxa in the ingroup (e.g. 21 of 24 speices)

o   Representative—samples across the diversity of morphology of the ingroup (e.g. 20 or 150 species, with at least one representative from each section)

o   Maxium parsimony (MP)—fewest changes represent the simplest and most probable tree

o   Maximum likelihood (ML)—finds tree that maximizes molecular probability of data

o   Bayesian—posterior probabilities of a model

o   Good papers use 2 or 3 of these methods, yielding similar results

o   All have different algorithms 

o   Akin to statistical analysis of support for each branching point in the phylogeny

o   Randomly selects characters from original datasets, and makes a tree from this sub-data set; repeated thousands of times

o   Counts percentage of trees with each monophyletic group present

o   Reports support in percentages

o   Nuclear

§  Biparental inheritance, recombines during crossing over and independent assortment

§  Coserved or variable

o   Plastid (chloroplast)=cpDNA

§  Uniparental (often mother/maternal), no recombination

§  Generally conserved

o   Mitochondrial=mtDNA

§  Uniparental (often maternal), no recombination

§  Generally highly conserved

§  rbcL—chloroplast (cpDNA) gene that codes for an enzyme that captures CO2 from atmosphere

·      rxns in photosynthetic pathway

·      some parasitic plants almost completely lack chlorophyll and live off host; but almost all others plants have this gene

§  ndhF—cpDNA gene that coes for NADH dehydrogenase

§  18S rRNA—nuclear gene that codes for a subunit of ribosomal RNA

§  conserved or of moderate variability

§  often useful at higher taxonomic levels

§  ribosomal genes are often conserved over time

§  rpL16—cpDNA intron of a ribosomal protein

·      generally of moderate variability

·      often useful among genera, species groups

·      more variable than DNA because accumulates mutations more (not selected against)

§  not transcribed, maintain proper distance between genes

§  trnL-F—spacer between the trnL and trnF genes (transfer RNA genes, very conserved_

·      often the most variable of all cpDNA regions

·      useful among genera, species, or subspecies

·      more variable because they are not transcribed or translated

§  recent publication date (~8-10 years)

§  intensive sampling of taxa

§  multiple genes/DNA regions

§  more than one genome sampled (nuclear, mt, or cp)

§  high bootstrap/jackknife support for groups

§  consistency across different kinds of analyses (MP, ML, Bayesian)