Bio HL1 Unit 3: Cladistics and Classification (A3.1/A3.2)

Organisms

an individual that can perform all the characteristics of life

characteristics of life

-organized structure

-reacts to stimuli

-can reproduce

-can grow/develop

-adapts to environments and evolves (through variation)

-maintains homeostasis

discrete (discontinuous) variation

Characteristics are in a few distinct categories, and is controlled by one gene locus (location) w/ few alleles

discrete variation example

Human blood types, biological sex, color blindness

Continuous variation

Characteristics are a range of values in between two extremes, that are controlled by multiple gene loci (locations)

continuous variation example

human height, mass, skin color

Morphological Species Concept (MSC)

Defines species as a group of organisms that are distinguished by a shared set of observable traits/features (look similar=same species)

Key features of MSC

-basis of classification (relies on phenotypes)

-historical foundation (originally used to create classification system)

-practicality (good for fossils and asexual organisms)

Limitations of MSC

-polymorphism (variation within a species)

-sexual dimorphism (males/females don't look alike)

-convergence

-cryptic species (identical but reproductively isolated)

Binomial Nomenclature

the formal naming system for species (created by Carl Linnaeus)

Rules of Binomial Nomenclature

-Genus name then species name

-Capitalization: Genus species

-Italics: all written in italics (underlined if hand written)

-Abbreviation: G. species

Why use binomial nomenclature?

-universal

-unique for each species

-indicates taxonomic relationships

-stable because latin is a dead language

Biological Species Concept (BSC)

Defines a species based on if they can reproduce together and are reproductively isolated from others

Limitations of BSC

-asexual reproduction ( some bacteria/archaea don't interbreed)

-Hybrids (infertile offspring)

-Geographic separation (allopatric population)

-Fossils and extinct species

-Ring species (like salamanders-no clear boundaries)

Difficulties for applying BSC

-Asexual Reproduction (ex: dandelions go through apomixis, their classification relies on MSC)

-Horizontal Gene Transfer in Bacteria (transfer of genes between organisms): transformation (uptake from environ.), transduction (transfer btwn by viruses), conjugation (transfer btwn cells through pilus).

Gradualism

Becoming a new species is not an instantaneous event but a long and slow accumulation of genetic changes.

Chromosomes

A thread like structure made of 1 DNA molecule, contains the base sequences that code for genetic instructions

How is the diversity of chromosomes a part of variation?

Each species has a unique number of chromosomes

Reduction division

The chromosome number is reduced by half (occurs during meiosis, fertilization restores number to diploid)

Karyotyping

Organizing/analyzing chromosomes by arranging them into pairs based on size, banding patterns, and centromere position.

Karyograms

Visual representation of chromosomes (constructed during metaphase)

Centromere

Where the sister chromatids connect

Banding patterns

Stains that reveal bands showing specific regions of DNA (unique to each chromosome)

Autosomes

Body chromosomes that DONT determine biological sex (chromosomes 1-22)

Chromosome abnormality example

Trisomy-21 (down syndrome)

-when there are 2 chromosome 21s (caused by non-disjunction)

types of centromeres

-metacentric (near middle)

-sub metacentric (off-center)

-acrocentric (near end)

-telocentric (at the end--not found in humans)

Chromosome 2 Fusion Hypothesis

Chrom. 2 arose from the fusion of chrom.12 and 13 (because other primates have 48 chroms. but humans have 46).

Telomeric sequences as Evidence for Chrom.2 Fusion

-Telomeres (protectice "caps" at the ends of chromosomes) are found in the middle of chrom.2

-typically only found at the ends of chromosomes.

Two centromeres as Evidence for Chrom.2 Fusion

-Chrom.2 has two centromeres

-one is inactive but there are still remnants of it being there

-Location of in chimps' chrom.12 matches humans' chrom.2

Banding Patterns & Homology as Evidence for Chrom.2 Fusion

-The banding patterns of chrom.2 match chimps' chrom.12 and 13

Matching Lengths as Evidence for Chrom.2 Fusion

-The length of Chimps' chrom. 12 and 13 match humans' chrom 2 when placed end to end

Evidence Against Chrom.2 Fusion

-lengths don't match perfectly

-centromere locus doesn't match perfectly

Gene

A sequence of DNA

Locus

Position of a gene on a chromosome

Genome

The entire set of genetic information found in an organism (including mitochondrial DNA in eukaryotes)

Single Nucleotide Polymorphisms (SNPs)

Single base differences in the DNA sequence between individuals

When is an SNP considered an allele?

When it occurs at a specific location at a frequency of +1%

How much of the genome do individuals of the same species share?

-Most (humans share 99.9%)

-0.1% contains variations

Causes of SNPs

-Errors during DNA replication (mistakes not corrected during cell division)

-Mutagens (environmental factors such as UV radiation or chemicals that damage DNA)

-Inherited Variations (passed down)

-Evolutionary Pressure (persist because of natural selection)

Neutral Effects of SNPs

-Affects non-coding regions (no effect on trait)

-Synonymous Changes (doesn't change amino acid sequence because of redundancy)

Functional Effects of SNPs

-Missense Mutations (SNPs in a region that alters amino acid sequence, affecting traits. Ex: sickle cell anemia, glutamic acid changed to valine)

-Nonsense Mutations (introduce premature stop signals, leads to nonfunctional protein bc process stopped too early)

Regulatory Effects of SNPs

-SNPs in promoter/enhancer regions (influence gene expression levels)

-Altered gene regulation can cause over/under/mis expression of important genes.

Disease Association as an Effect of SNPs

-SNPs can increase susceptibility to diseases/disorders (ex: SNPs in APOE gene can lead to alzheimers)

-SNPs can also protect against diseases

Pharmacogenomics as an Effects of SNPs

-SNPs can influence how individuals metabolize drugs/respond to treatments (ex: variations in CYP2C19 gene)

Evolutionary Effects of SNPs

SNPs lead to variation

C-Value Paradox

When total DNA content (C) varies between species and doesn't correlate w/ organism complexity

Dichotomous Keys

A tool used to identify/classify organisms based on their physical characteristics

Features of Dichotomous Keys

-yes/no questions (binary choices)

-sequential steps

-focuses on observable/measurable traits

-hierarchial structure (broad to specific)

DNA barcoding

-Sequences a short, standard region of DNA and turns it into a unique barcode in a database

Advantages of DNA barcoding

-accurate

-rapid identification

-scalable

-efficient

Environmental DNA (eDNA)

Genetic material shed by organisms into the environment (skin, feces, mucous)

Advantages of eDNA

-non invasive

-comprehensive

-efficient

Taxonomy

Classifies organisms based on their shared characteristics

Taxonomy Classification System (DKPCOFGS)

-Domain

-Kingdom

-Phylum

-Class

-Order

-Family

-Genus

-Species

Benefits of Classification System (taxonomy)

-organizes biodiversity

-shows evolutionary relationships

-Identifies

-Helps conservation

-Enables predictability

Limitations of Traditional Classification System

-Based on morphology not evolutionary relationships

-Doesn't account for convergence

-Limited use of genetic evidence

-Organisms don't fit neatly into one category

-Difficult to classify microorganisms (because of HGT)

Advantages of Newer Classification System

-Reflects common ancestry

-More accurate/objective

-Predictive power bc of similarities

-Helps understand evolutionary processes

-Better representation of biodiversity

-Consistent w/ molecular bio

-Reduces misclassification

Clade

A group of organisms that includes a common ancestor and all its descendants

Cladogram

Visual representation of evolutionary relationships (clade represented by a branch, point of split called a node)

Type of evidence used in cladograms

genetic (to determine ancestry), fossil, embryological (similarities in development)

Things used to determine clade divergence

-Molecular clock (assumes mutations accumulate at a steady rate)

-Genetic differences (resulting from mutations)

-parsimony (principle that the simplest explanation w/ the fewest evolutionary changes is the most likely, best cladogram has fewest mutations)

Features of a cladogram

-Root: the common ancestor at beginning of cladogram

-Outgroup: The most distantly related species

-Taxa: Ends of branches, individual species

-Node: point of divergence

Example of Species Reclassification

Figwort

-Figwort family was very big and included about 275 genera (pl. of genus), it was based on flower structure (morphological trait)

-DNA sequencing showed that species were not closely related at the genetic level

-Convergent evolution caused them to look similar

-Figwort family was split and reclassified into many families (ex: plantains and broomrapes)

How are living organisms primarily classified

Into 3 domains based on ribosomal RNA (rRNA) sequences

Bacteria (domain)

prokaryotes w/ peticloglycan cell walls and simple structures

Archaea (domain)

prokaryotes that are genetically distinct from bacteria (often live in extreme environments)

Eukarya (domain)

organisms with membrane bound organelles (protists, humans, plants, fungi)

Evidence for 3 Domains Researcher

-Provided by Carl Woese (1977), determined archaea were more related to eukarya than bacteria by sequencing rRNA

Evidence for 3 Domains

-Archaea ribosomal structure, lipid membrane, and gene expression machinery are more similar to Eukarya than to bacteria

-There are unique biochemical pathways and enzymes in each group

-rRNA sequences of Archaea share more similarities with Eukarya than with bacteria

3 Domains and Common Ancestry

-Bacteria branched off from LUCA first

-Arch. & Euk. share a more recent common ancestor