Phylogeny

Phylogeny

Evolutionary history of a group of organisms

Tree of Life

Universal phylogenetic tree

Use of phylogenetic trees

• Defining species

• Tracking diseases

• Fingerprinting

If there are more common traits then

There is a more recent common ancestor

Root

Most ancestral branch on the tree

Taxon/Taxa

Individual/branch tip that can be at any scale

Nodes

Divergence from ancestor in different lineages

Internode

In betwen nodes

Branch

Node to tip

Outgroup

Group sharing common ancestor but not part of studied group

Extant Taxa

Currently living

Sister Groups

Share common ancestor

Polytomy

Nodes diverging into 3+

Ancestral Trait

Trait existing in ancestor

Derived Trait

Modified form of ancestral trait in descendent

Cladistic Approach

Organization based on synapomorphies

Parsimony

Most likely tree is the one that’s least complicated

Homoplasy

Traits are alike for reasons other than common ancestry

Polyphyletic Group

Group that doesn’t include most recent common ancestor

Paraphyletic Group

Includes ancestral population but not all descendants

Mass Extinction

At least 60% of species on the world are wiped out in 1 mill years

Background Extinction

Certain populations are reduced to 0 from normal processes

End Permian/Great Dying

90% of species died from O2, SO3 levels, acid rain, toxic ash

Adaptive Radiation

Rapid production of many descendant species that range morphologically from a single lineage

Characteristics of Adaptive Radiation

1. A part of monophyletic group

2. Speciated rapidly

3. Diversified quickly into niches

Ecological Opportunity

Availability of more or new types of resources, driving wide array of adaptive radiation

Examples of Adaptive Radiation

• Hawaiian plants

• Anolis Lizards

Anolis Lizards

Short leg twig vs long-legged trunk lizard, all islands speciated into same species regardless of colonizing forms

Coevolution

Reciprocal evolutionary change in interacting species, resulting in adaptations within lineages (eg: plants + herbivores)

Cambrian Explosion

Quick diversification of species documented by fossils in Canada, China, Australia

Fauna

Collection of animal species

Ediacaran Period

Consists of sponges, corals, no shells or heads

Cambrian Period

Creation of predators, scavengers, movement

Triggers of Cambrian Explosion

• Higher O2 levels making areobic possible

• Predation (selection)

• New niches

• New genes, new bodies

HOX Genes

Group of genes that regulate development of animal’s body plan, especially along head to tail axis.

Burgess Shall Fossilize Organisms

500 million years age, preserving soft tissue, sensory organs

Hominids

Great apes with distinct ways of walking either fist or knuckle

Hominins

Monophyletic group with Homo Sapiens and synapomorphy of bipedalism

Ardipithecus Ramidus

4.4 mya, earliest known hominin

Hominins Group

1. Gracile australopithecines

2. Robust australopithecines

3. Early homo spaiens

4. Recent homo sapiens

Australopithecus

Around 4.5-1 mya, small teeth, bipeds

Paranthropus

Around 2.7-1 mya, big teeth, herbivores

Homogenus Habilis

Around 2.3 mya, first homo, tools, parents of Homo erectus, Neanderthals, and sapiens

Homo Erectus

Around 1.8 mys, fire use, migrated out of Africa

Homo Neaderthalensis

Around 400-24 kya, lived with homo sapiens

Homo Sapiens

Around 195 kya, flat face, big brain

Multiple Species of Hominins

Lived on Earth at the same time

Homo Sapiens were selected for

Communication and reasoning from increased tool and language use

Out of Africa Hypothesis

H Sapiens evolved in Africa then dispersed to Europe/Asia where species evolved

While H Sapiens occupied Africa

Neanderthalensis resided in Europe and Middle East

Neanderthalensis went extinct

After thousand of years of coexistence with H Sapiens in Europe

1st Movement

East + South to Australia

2nd Movement

Europe + Asia

Bipedalism Advantages

• Lower SA

• Hands Free

• Long Distance Migration

Physiological Changes in H Sapiens

• Position of foreman magnum enters below

• Bowl shaped pelvis for balance/posture

• Arched feet and no opposable toe

Male Gorillas

Doubled in weight of females

Gibbon Males

Same size as females

Human Males

15% Larger

Speech Mutation

FOXP2 mutation + hyoid bone for tongue movement

Reciprocation

Fitness feedbacks in small groups, benefitting other feeds back to benefit you (cooperation)

Most genetic variaiton exists in

Individuals

Selective Agents for Dark Skin

• Skin cancer (melanoma vs non melanoma)

• Folate levels

• vitamin D

Folate

Needed for DNA repair, synthesis, gamete development which UV rays breakdown folate in blood

Vitamin D

UV rays needed for synthesis which regulates immune system

Malaria

Plasmodium via mosquitoes

Hemoglobin HbS Mutation

Sickled shaped blood cells (heterozygous selection)

Pastoralism

Domestication of dairy animals that spread to Europe and lactase persistence evolved independently

Hygiene, Old Friend Hypothesis

Hygiene practices have changed, causing microbiome relationships within our bodies to change

Modern Practices have removed

Coevolved microbiota, leading to immune system dysregulation

Autoimmune Disorders licked to

Removal of worms that dampen inflammatory responses

Estrogen/Progestrone Contraception

More cycles in lifetime, meaning breast tissue undergoes more mitosis causing changes of mutations and breast cancer (but decreases ovarian cancer)

Selection Intensity

Decreases with age

Mutations that Improve Reproduction

Is selected for, even at expense of performance later in life

Antagonistic Pleiotropy

Animals have genes that enhance fitness early in life, but diminish in life

Bacteria resistance caused by

Horizontal gene transfer

Efflux Pumps

A protein that removes drugs from cell

Phage Therapy

Using phages to implant and burst bacteria

Phage Therapy and Drug Resistance

Bacteria becomes immune to phages, possibly increasing antibiotic sensitivity, levraging fitness trade off