Species Identification and Classification

• Identifying species is important for farmers, gardeners, doctors, and border inspection officials
• Farmers and gardeners need to identify harmful weeds
• Doctors need to identify bacterial strains for correct medication
• Border officials prevent the entrance of invasive species

Species Concepts

• Morphological species concept: compares morphology between similar organisms using body shape, size, and other features
• Advantage: simplistic and widely used, especially for plants
• Disadvantage: it can be hard to know how much variation is too much as populations are made of non-identical individuals
• Biological species concept: focused on the ability of organisms to interbreed and produce viable, fertile offspring
• Advantage: widely used
• Disadvantage: cannot be applied in all cases, for example, rabbits separated by geographical location
• Phylogenetic species concept: examines the evolutionary history (phylogeny) of an organism
• Defines a species as a cluster of organisms distinct from other clusters
• Similarities in genetic codes can prove species relatedness and aid classification
• Advantage: DNA analysis is very accurate and can be used with extinct species
• Disadvantage: Evolutionary history is not known for all species

Taxonomy

• Taxonomy is the branch of biology that identifies, names and classifies species based on natural features
• Carolus Linnaeus is the father of taxonomy
• Binomial nomenclature: a two-part naming system
• The first word is the genus name, the second is the species name
• Scientific names are italicized when typed and the genus name is capitalized
• When handwritten, both parts must be underlined
• Classification: the grouping of organisms based on a set of criteria to organize and indicate evolutionary relationships
• Hierarchical classification classifies by arranging species into categories from general to specific which is known as a nested system
• Each level of category in the hierarchy is called a rank
• The specific classification of an organism at each rank level is called the taxon

Determining Species Relationships

• Evolutionary history and relationships are determined by:
• Anatomical evidence: study of the structure and form of organisms, including internal systems
• Physiological evidence: physical and chemical functions, internal processes like protein, and insulin synthesis. Protiens are determined by DNA
• DNA evidence: comparing DNA sequences from different species

Phylogenetic Trees

• Phylogenetic trees are branching diagrams showing evolutionary relationships
• Species are grouped into clades and species at the bottom of the tree are older

Importance of Classification

• Classification is important for:
• Discovering new drugs, hormones, and other medical products
• Tracing disease transmission and treatment development
• Increasing crop yields and disease resistance
• Environmental conservation, protecting rare species

Hierarchy of Taxa

• The hierarchy of taxa from broadest to most specific is:
• Domain
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species

Domains

• Domain: The highest level
• Three domains: archaea, bacteria, eukarya
• Six kingdoms: bacteria, archaea, plantae, animalia, fungi, protista

Prokaryote vs. Eukaryote

• Prokaryotes
• Size: 1-10 um
• Genetic Material: Circular DNA, not bound by a membrane; genome made up of single chromosome
• Cell Division: not by mitosis and meiosis
• Reproduction: asexual reproduction common
• Number of Cells: unicellular
• Organelles: mitochondria and other membrane-bound organelles absent
• Metabolism: mostly anaerobic (does not require oxygen)
• Eukaryotes
• Size: 100-1000 um
• Genetic Material: DNA in nucleus bounded by a membrane; genome made up of several chromosomes
• Cell Division: by mitosis and meiosis
• Reproduction: sexual reproduction common
• Number of Cells: mostly multicellular
• Organelles: mitochondria and other membrane-bound organelles present
• Metabolism: mostly aerobic (does require oxygen)

Dichotomous Key

• An identification tool consisting of a series of two-part choices that lead the user to a correct identification

Archaea vs. Bacteria

• Prokaryotes are represented by Bacteria and Archaea
• Common forms:
• Coccus (spherical)
• Bacillus (rod)
• Spirillum (spiral)
• Aggregations:
• Diplo (cells arranged in pairs)
• Strepto (cells arranged in a chain)
• Staphylo (cells arranged in clusters)

Nutrition

• Autotroph: obtains energy by making its own food (e.g., sunlight)
• Heterotroph: cannot make its own food and gets nutrients from consuming other organisms
• Unique to archaea: methanogenesis produces methane
• Unique to bacteria: photosynthesis converts water and carbon dioxide into sugars and oxygen (e.g., cyanobacteria)
• Habitats:
• Archaea are extremophiles (live in extreme conditions)
• Bacteria are mesophiles (live in moderate conditions)
• Thermophile: archaea that live in high-temperature environments
• Halophile: archaea that live in very salty habitats
• Acidophile: archaea that live in acidic conditions
• Reproduction:
• Prokaryotes reproduce asexually through binary fission where a cells divides into two identitical cells
• Some bacteria and archaea exchange DNA through conjugation with a pilus
• They may have small DNA loops called plasmids.
• Classifying prokaryotes:
• Size and shape
• Nutrition
• Movement
• Genetic components

Gram Stain

• Divides most bacteria into groups
• Gram-positive bacteria have a thick protein layer in their cell wall and stain purple
• Gram-negative bacteria have a thin protein layer in their cell wall and stain pink/red.

Protists

• Protists are unicellular eukaryotes that aren't fungi, plants, or animals

Protist Groups

• Animal-like protists:
• Often called protozoans, are heterotrophic and consume prokaryotes, other protists, or organic wastes
• Some are parasitic, consuming nutrients from the organism they live in
• A parasite is an organism that benefits by living in or on another organism at the expense of that organism
• Fungus-like protists:
• Heterotrophs
• Absorb nutrients from living organisms, dead organisms, and wastes
• Produce spores and are classified as slime molds or water molds
• Plant-like protists:
• Contain pigments like chlorophyll in their chloroplasts for photosynthesis
• Some consume other organisms when light is unavailable
• Unicellular, plant-like protists: diatoms, dinoflagellates, and euglenoids

Algae

• Photosynthetic protists which can be unicellular or multicellular
• Multicellular algae are seaweeds, classified into 3 phyla (brown, red, and green) by color
• Green algae represent the evolutionary link between protists and plants

Algae Types

• Brown algae: anchored by a holdfast, with a stipe extending from the holdfast
• Red algae: first multicellular species, containing phycoerythrin (red pigment)
• Green algae: resemble plants, with cellulose cell walls and similar chlorophyll molecules

Shift to Land

• Evidence suggests that green algae and land plants are related
• Both contain chlorophyll
• Both have cellulose-based cell walls
• Both store food as starch
• Show genetic similarities
• Green algae use reproductive strategies used by some plants
• Embryos: small, simple, multicellular plants dependent on the parent plant

Vascular Tissue

• Early terrestrial plants lacked tissues to transport materials over large distances
• Vascular plants emerged
• Phloem tissue transports sugars
• Xylem tissue transports water and minerals, and allows plants to grow to great heights due to the tough lignin within
• Leaves are specialized structures to maximize light capture

Plant Kingdom

• Based on the presence/absence of:
• Vascular tissue
• Seeds
• Non-vascular plants (bryophytes):
• mosses, liverworts, and hornworts
• They lack vascular tissue and depend on diffusion and osmosis
• Mosses thrive in bogs, tundra, and shade
• Liverworts grow in moist, shady places, rotten wood, and soil
• Hornworts live on tree trunks, riverbanks, and in other damp locations
• Seedless vascular plants:
• Whisk Ferns
• Club mosses
• Ferns
• Horsetails
• Seed-producing vascular plants:
• Gymnosperms
• Angiosperms

Plant Diversity

• Gymnosperm: vascular plant with non-enclosed seeds
• Angiosperm: vascular plant with seeds enclosed in protective issue

Seed Usefulness

• Plants use seeds for:
• Sexual reproduction without water
• Protection against harsh environments
• Survival for many years without water
• Survival in colder temperatures
• Seed dispersal across continents
• Gymnosperm diversity:
• Cone-bearing species (pines, firs, yew, cedars, redwoods)
• Angiosperm diversity (flowering plants):
• Includes over 250,000 species (90% of all plants)
• Reproduce using flowers and their seeds are protected in fruits (roses, trilliums, maps, oaks, birches, and grasses)

Angiosperm Features

• Fruits are specialized structures that disperse seeds
• Attract animals
• Have adaptations for sticking to fur
• Protective enclosures for seeds dispersed by water
• Two main groups:
• Seed leaf or cotyledon: nourishes the plant from the embryo that allows it to initially grow
• Monocot: a major cluster of flowering plants that only has one cotyledon
• Dicot: major cluster of flowering plants that only has two cotyledons

Fungus Kingdom

• Fungus: a heterotrophic eukaryotic organism with chitin cell walls
• Hyphae: a multicellular, thread-like filament that makes up the structural unit of a fungus
• Mycelium: extends below ground for nourishment
• Fruiting body: made of hyphae, spore-reproducing, a reproductive structure

Fungal Reproduction

• Asexual (unicellular):
• Spore production
• Budding (unicellular yeasts)
• Smaller cell develops while attached to the parent cell. Eventually gets pinched off
• Fragmentation - piece of mycelium breaks off
• Sexual (multicellular): Trillions of spores produced and released by the fruiting body
• Fungal nutrition: Fungi release enzymes, they absorb nutrients through cell membranes
• Classifying fungi: By reproduction (sexual or asexual) and by the structure of the fruiting body
• Fungi imperfecti: phylum deuteromycota includes fungi that do not reproduce sexually and is an important source for pharmaceuticals