Phylogeny, Plant Diversity, and Structure Overview

Phylogeny

The evolutionary history of a species or group of related species.

Use of phylogenies

Helps scientists understand evolutionary relationships and construct phylogenetic trees.

Systematics

A branch of biology that classifies organisms and determines their evolutionary relationships.

Binomial nomenclature

A system for naming species using two parts: genus and species.

Components of binomial name

Genus (capitalized) and Species (lowercase).

Taxonomic categories

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

Mnemonic for taxonomic categories

Dear King Philip Came Over For Good Spaghetti.

Organisms in same order vs same phylum

Same order → More specific category than phylum.

Branch point in a phylogenetic tree

A common ancestor from which two lineages diverged.

Sister taxa

Groups that share an immediate common ancestor and are each other's closest relatives.

Phylogenetic tree orientation

It can be horizontal, vertical, or diagonal—only the branching pattern matters, not the orientation.

Humans related to frogs or lizards

Lizards → Humans and lizards share a more recent common ancestor than humans and frogs.

Rooted phylogenetic tree

A rooted tree has a branch representing the most recent common ancestor of all taxa in the tree.

Fishes as basal taxon

They are the earliest diverging lineage in a given tree.

Key points about phylogenetic trees

Actual ages of species, exact amount of genetic change, whether one taxon evolved from another cannot be determined.

How phylogenetic trees are inferred

By analyzing morphological (physical) and molecular (DNA/protein) similarities.

Homologous structures

Similar due to shared ancestry (e.g., whale fin & bat wing).

Analogous structures

Similar due to convergent evolution (e.g., bird wing & butterfly wing).

Importance of distinguishing structures

Only homologous traits should be used to infer evolutionary relationships.

Determining DNA homologies

By aligning gene sequences and identifying conserved regions.

Species A, B, and C relation

B and C (genetic similarity is more reliable than appearance).

Clade

A group including an ancestor and all its descendants (monophyletic group).

Group I monophyletic

It includes a single ancestor and all its descendants.

Group II paraphyletic

It includes an ancestor but not all descendants.

Group III polyphyletic

It includes taxa with different ancestors.

Shared derived character

A new trait that evolved in a clade but not in ancestors.

Hair as shared derived character

Hair evolved in mammals only (derived), while backbones appeared earlier (ancestral).

Lancelet as outgroup

It shares the fewest derived characters with the other taxa.

Animals in clade with four limbs

Amphibians, reptiles, birds, and mammals.

Maximum parsimony in phylogenetic trees

The simplest explanation (fewest evolutionary changes) is most likely correct.

Phylogenetic tree representation

A hypothesis about evolutionary relationships.

Evidence suggesting birds are related to crocodiles

DNA, fossil evidence, and shared derived traits (e.g., similar heart structure, nest-building behavior).

Genome's role in evolutionary relationships

DNA sequences reveal genetic similarities and divergence over time.

Method showing fungi are related to animals

rRNA gene comparison (changes slowly over time).

Method revealing Native American ancestry

Mitochondrial DNA (mtDNA) (evolves quickly).

Orthologous genes

Genes in different species from a common ancestor (e.g., human and mouse hemoglobin genes).

Paralogous genes

Genes duplicated within a species that evolve independently (e.g., human hemoglobin genes).

Mice as model organisms for human diseases

They share many homologous genes with humans.

Conserved genes

They remain unchanged over time, indicating descent from a common ancestor.

Molecular clocks

Models that estimate the time of evolutionary divergence based on DNA mutations.

How molecular clocks work

Assume mutations accumulate at a constant rate over time.

Emergence of HIV according to molecular clocks

Around 1930.

Problems with molecular clocks

Mutation rates are not always constant.

Key derived characters of plants

Plants evolved from green algae (charophytes).

Five key traits shared with green algae

Rings of cellulose-synthesizing proteins, peroxisome enzymes, structure of flagellated sperm, formation of a phragmoplast, sporopollenin (prevents drying out).

Sporopollenin

A polymer that protects spores and zygotes from drying out, allowing colonization of land.

Alternation of generations in plants

Key events: Fertilization and meiosis; Gametophyte (n) → produces gametes via mitosis; Sporophyte (2n) → produces spores via meiosis.

Derived traits of plants for terrestrial life

Sporangia: Organs where spores are produced; Spores: Haploid cells that grow into gametophytes; Cuticle: Waxy layer that prevents water loss; Apical meristems: Regions of active growth in roots and shoots; Stomata: Pores for gas exchange; Vascular tissue: Conducts water and nutrients; Seed: A plant embryo with a food supply and protective coat.

Gymnosperms

Plants with 'naked' seeds (e.g., pine trees).

Angiosperms

Flowering plants with seeds in fruit (e.g., apple trees).

Life cycle of nonvascular plants (Bryophytes)

Dominant generation: Gametophyte (haploid, n).

Reproductive structures of nonvascular plants

Antheridium: Produces sperm; Archegonium: Produces eggs; Sporophyte (2n) produces spores via meiosis.

Spore dispersal in nonvascular plants

By wind or water.

Fertilization in nonvascular plants

Requires water; sperm swims to egg.

Seedless vascular plants

First plants to grow tall due to vascular tissue.

Xylem

Transports water and minerals

Phloem

Transports sugars and nutrients

Competitive Advantage of Vascular Plants

Grow taller → better access to sunlight

Structural support from lignin

Provides support to vascular plants.

Roots

Absorb water and anchor plants

Leaves

Increase surface area for photosynthesis

Dominant Generation

Sporophyte (diploid, 2n)

Moist Environment Required

Sperm needs water to reach the egg.

Three Components of a Seed

Embryo - Young developing plant

Food Supply

Provides nutrients.

Seed Coat

Protection.

Five Common Characteristics of Seed Plants

Reduced gametophyte stage.

Heterospory

Microspores & megaspores.

Ovules

Structures that develop into seeds.

Pollen production

The process of creating pollen grains.

Pollen

Eliminates need for water for fertilization.

Seeds

Provide protection & nourishment, allow dormancy.

Advantages of Miniaturized Gametophytes

Protection from environmental stress.

Dependent on sporophyte for nutrients

Miniaturized gametophytes rely on sporophytes.

No need for water for fertilization

Miniaturized gametophytes do not require water.

Enhanced dispersal mechanisms

Improved methods for spreading gametophytes.

Megaspore

Develops into female gametophyte → Produces eggs.

Microspore

Develops into male gametophyte → Produces sperm.

Pollination Purpose

Transfer of pollen to ovules for fertilization.

Advantages of Pollen Over Free-Swimming Sperm

No dependence on water.

Increased dispersal distance

Pollen can travel further than sperm.

Advantages of Seeds Over Spores

Can remain dormant until favorable conditions.

Contain stored food for the embryo

Seeds provide nourishment for developing plants.

Can be transported long distances

Seeds can move away from the parent plant.

Four Phyla of Gymnosperms

Cycadophyta (cycads).

Ginkgophyta

Ginkgo biloba.

Gnetophyta

Ephedra, Gnetum, Welwitschia.

Coniferophyta

Conifers: pines, firs, spruces.

Five Examples of Coniferophyta

Pines.

Firs

A type of conifer.

Spruces

Another type of conifer.

Redwoods

Large conifer trees.

Cedars

A type of conifer.

Gymnosperm Life Cycle

Sporophyte (tree) produces cones.

Male cones

Make pollen; female cones make ovules.

Wind pollination

Transfers pollen.

Fertilization

Occurs inside ovule.

Seed forms & disperses

The process of seed development.

Seed germinates into new sporophyte

The seed develops into a new plant.

Why Gymnosperm Seeds Are "Naked"

They are not enclosed in fruits (develop on cone scales).