Week 14: History Of Life And Human Evolution

Fossil

Any preserved remains, impression, or trace of any once-living thing from a past geological age.

Ex: bones, shells, exoskeletons, imprints of animals or microbes

• Formed when: Organisms buried quickly, during rock formation, hard parts of organisms replaced by minerals

• Vast majority of fossils are NOT the organisms themselves.  Rather, impressions or trace of once-living organism

Hybridization

The crossing of two genetically different plant species, varieties, or genera to produce hybrid offspring.

Ex: Hybridization between ancient humans and Neanderthals

• Neanderthal and Denisovian DNA in genomes of modern humans

• Neanderthal and Denisovian DNA affects human health

Mass extinction

A mass extinction event is when species vanish much faster than they are replaced. This is usually defined as about 75% of the world's species being lost in a short period of geological time

Local adaptation

 Different traits are selected for in different parts of a species range.

How do you know? genes with different alleles in different populations

Examples of local adaptation in humans:

• Lactase persistence (populations with dairy animals) 

• Skin color (closer to equator protection against UV, 

maintain vitamin D synthesis in higher latitudes)

• Many examples of local adaptation to pathogens (e.g. malaria).

• High altitudes

Adaptive introgression

The transfer of genetic material between distantly related lineages through gene flow increases the fitness of the recipient lineage.

• ~ 3% of DNA in Icelandic genomes is from Denisovans – perhaps via  Neanderthal introgression (Nature, 2020)

Endosymbiosis Theory

some of the organelles in eukaryotic cells were once prokaryotic microbes. Mitochondria and chloroplasts are the same size as prokaryotic cells and divide by binary fission. Mitochondria and chloroplasts have their own DNA which is circular, not linear.

• Eukaryotic Cell, perhaps the greatest evolutionary innovation

  appeared ~ 1.8 BYA

Transitional form/feature

A fossil that shows an intermediate state between an ancestral trait and that of its later descendants

Radiometric dating

Calculates an age in years for geologic materials by measuring the presence of a short-life radioactive element, e.g., carbon-14, or a long-life radioactive element plus its decay product

Homo neanderthalensis

Neanderthals are an extinct group of archaic humans who inhabited Europe and Western and Central Asia during the Middle to Late Pleistocene. Neanderthal extinction occurred roughly 40,000 years ago

Selective sweep

A selective sweep is the process through which a new beneficial mutation that increases its frequency and becomes fixed (i.e., reaches a frequency of 1) in the population leads to the reduction or elimination of genetic variation among nucleotide sequences that are near the mutation

Exam question:  Identify seven major events in the history of biodiversity and identify when (mya, bya, kya) these events happened

Text Figure 26.4

1. 3.8-3.5 bya. single-celled microbial life (prokaryotes) is found in rocks

2. 3.5 bya. Great Oxygenation Event (GOE): Cyanobacteria - oxygenic photosynthesis, leading to oxygen accumulation in the atmosphere

3. 1.8 bya. Evolution of Complex Cells (Eukaryotes): Complex cells with a nucleus and specialized organelles (eukaryotic cells)

4. 1.5 bya. Multi-celluar organisms began to appear

5. 632 mya. first animals began to appear

6. 533-525 Cambrian Explosion: A rapid diversification of life occurred during the Cambrian Period

7. ?

Or based off ai cause yk

• First Life Appears: The earliest undisputed evidence of simple, single-celled microbial life (prokaryotes) is found in rocks dating back at least 3.5 bya.

• Great Oxygenation Event (GOE): Cyanobacteria began oxygenic photosynthesis, leading to oxygen accumulation in the atmosphere, starting around 2.4 bya. This event was toxic to many existing anaerobic life forms and fundamentally changed the planet's environment, setting the stage for future complex life.

• Evolution of Complex Cells (Eukaryotes): Complex cells with a nucleus and specialized organelles (eukaryotic cells) appeared around 1.8 bya, a major step towards multicellularity.

• Cambrian Explosion: A rapid diversification of life occurred during the Cambrian Period, starting around 541 mya, when nearly all major animal phyla (basic body plans) first appeared in the fossil record.

• First Colonization of Land by Plants: Land plants evolved around 475 mya (Ordovician/Silurian periods), creating new habitats and food sources that allowed animals to eventually colonize land.

• End-Permian Mass Extinction ("The Great Dying"): The largest mass extinction event in Earth's history occurred about 251 mya, wiping out approximately 96% of marine species and 70% of terrestrial vertebrate species and completely resetting the evolutionary trajectory of life.

• End-Cretaceous Mass Extinction: A major extinction event, likely caused by an asteroid impact, occurred 66 mya, leading to the extinction of non-avian dinosaurs and paving the way for the rapid diversification and dominance of mammals. 

The fossil record is incomplete. Which of the following are reasons for this incompleteness?

1. Fossils of larger organisms are more likely to be found than fossils of smaller organisms

2. Paleontologists are more interested in some species than others

3. Species with larger population sizes over larger geographic areas are more likely to be in the fossil record than species with small population sizes

4. All of the above

 

4. All of the above

Life on earth began approximately 

1. 3.7 billion years ago C.  2.7 billion years ago

2. 300 million years ago D.  6,000 years ago

1. 3.7 billion years ago

The endosymbiosis hypothesis explaining the evolution of eukaryotic cells is supported by:

1. the presence of DNA in mitochondria and chloroplasts

2. DNA-sequence analyses comparing bacterial genomes, mitochondrial genomes, and eukaryotic nuclear genomes

3. naturally occurring endosymbiotic relationships between bacterial and eukaryotic cells

4. All of the above

4. All the above

Fossils are usually dated by:

1. Analyses of radioisotopes of igneous rocks found near the fossil

2. Genome similarity between fossil DNA and modern DNA

3. Timing of continental drift

4. Analyses of radioisotopes of the fossil

1. Analyses of radioisotopes of igneous rocks found near the fossil

The earth’s atmosphere today

1. has much higher levels of O2 (oxygen) than it did before the evolution of photosynthetic organisms

2. is very similar to what it has been for the past 4 billion years

3. is likely quite different than it was 4 billion years ago, but we do not know any of those differences

4. none of the above

1. has much higher levels of O2 (oxygen) than it did before the evolution of photosynthetic organisms

Prokaryotes

1. include both bacteria and archaea

2. evolved from single-celled eukaryotes

3. Include only bacteria

4. None of the above

1. include both bacteria and archaea

• Prokaryotes lack a nucleus

Which of the following is correct?

1. Humans are more closely related to Orangutans than they are to Monkeys

2. Humans are more closely related to Monkeys than they are to Gorillas

3. Humans are more closely related to Orangutans than they are to Gorillas

4. Humans are more closely related to Gorillas than they are to Chimpanzees

 

1. Humans are more closely related to Orangutans than they are to Monkeys

Primates evolved from small arboreal insect-eating mammals

1. About 10 MYA

2. At about the same time that terrestrial plants evolved

3. Before dinosaurs went extinct

4. All of the above

3. Before dinosaurs went extinct

1. Humans last shared a common ancestor with their most closely related extant primate relative approximately

1. 200,000 years ago B.  3 MYA C.  7 MYA D.  10 MYA

1. C.  7 MYA

Data support which of the following:

1. humans interbred with both Homo neanderthalensis and Denisovans

2. humans (H.sapiens) did not interbred with any other hominid species

3. humans interbred with H. neanderthalensis, but not other hominid lineages

4. the human genome is a mix of at least 5 now extinct hominid lineages

1. humans (Homo sapiens) interbred with both H. neanderthalensis and Denisovans

Homo sapiens originated in the part of the world that we refer to as:

1. Africa C.  Europe

2. Asia D.  North America

1. Africa

The movement of landmasses that has changed their positions, shapes, and association with other landmasses is called

1. plate tectonics C.  Pangea

2. glaciation D.  biogeography

 

1. plate tectonics

1. Which of the following evolutionary innovations was advantageous for survival in a terrestrial environment?

1. The amniotic egg in animals C.  The seed in plants

2. Both of the above D.  None of the these.

1. Both of the above

he earth is approximately how old?

1. 450 million years C.  1.5 million years

2. 4.5 billion years D.  6.0 billion years

1. 4.5 billion years

On the map below, draw the major historical migrations of Homo sapiens (i.e. the migrations that resulted in the spread of H. sapiens across the world).  Provide approximate times (years before present) of four of those migrations.

1. Homo neanderthalensis was determined to be distinct from H. sapiens (humans) based on fossilized bones.  H. denisovan was identified as a species using ancient DNA.  Analyses of human genomes and ancient DNA from H. neanderthalensis and H. denisovan, reveal that hybrids between any of these three species produced viable and fertile offspring.  Based on this information, answer the following: 

By what species concepts are H. sapiens and H. neanderthalensis distinct species?

Biological Morphological           Phylogenetic

By what species concepts are H. sapiens and H. denisovan distinct species?

Biological Morphological           Phylogenetic

By what species concepts are H. neanderthalensis and H. denisovan distinct species?

Biological Morphological           Phylogenetic

By what species concepts are H. sapiens and H. neanderthalensis distinct species?

Biological Morphological           Phylogenetic

By what species concepts are H. sapiens and H. denisovan distinct species?

Biological Morphological           Phylogenetic

By what species concepts are H. neanderthalensis and H. denisovan distinct species?

Biological Morphological           Phylogenetic

1. Which of the following processes contribute to the evolutionary divergence of populations? 
   

1. Allopatry

2. Sympatry

3. Hybridization

4. Selection

5. Gene flow

6. Genetic drift

7. Mutation

8. Pleiotropy

4. Selection

6. Genetic drift

7. Mutation

The fossil record is incomplete.  This is not surprising.  Identify four factors that contribute to the probability a species is found in the fossil record.

Organisms size

Paleontologists’ interest

Population size 

Habitat in which organism lived

Age

1. Identify when seven of the events below are estimated to have happened (note, “first appear” means “first appear in the fossil record”).. 
   

______  Cambrian explosion

______  Homo sapiens first appear

______  First fossils of cyanobacteria

______  Flowering plants first appear

______  Hominids first appear

______  Seed plants first appear

______  Dinosaurs go extinct

______  Birds first appear

______  First Animals appear

______  Large-scale colonization of land by plants

______  Shelled animals appear

______  Dinosaurs first appear

______  Multicellular eukaryotic organism appear

______  Eukaryotic cells first appear

______  Prokaryotic cells first appear

______  Mammals first appear

______  Reptiles first appear

______  Large-scale terrestrial colonization by 

animals

______  First vertebrates

______  First land plants

______  other ______________________

 Draw two trees.  The first should show the correct relationships among gene 7 gene sequences, one sampled from a gorilla, one from a Neanderthal, one from a chimpanzee, and four from humans.

The second tree should show the correct relationships among gene 7 gene sequences, one sampled from a gorilla, one from a Neanderthal, one from a chimpanzee, and four from humans – with one of the alleles that was sampled from a human was derived from a Neanderthal. Label where each sequence is on the tree.

For each of the following, what can you infer about selection? 

a.       The DNA sequences of a chimp and human protein coding gene are identical.

b.       A comparison of DNA sequences of a protein coding gene from chimp, gorilla, and human reveals 10 differences between human and gorilla, 30 differences between human and chimp, and 60 differences between gorilla and chimp.

c.       The DNA sequences of a chimp and human protein coding gene differ at 16 nonsynonymous (replacement) sites and 2 synonymous (silent) sites.

d.       In a sample of 40 human genomes, a 400,000 bp region has no polymorphic sites.  (Based on genome-wide sequence data (i.e the sequence of the entire genome), one expects that the genomes of two randomly chosen humans will have approximately 1 polymorphic site every 1,000 bp.)

e.   The genome of an individual living in Germany has a 300,000 bp region that is more similar to the homologous region of a Neanderthal genome than it is to the same region of most modern human genomes.

f.    A comparison of DNA sequences of a protein coding gene from chimp, gorilla, and human reveals 30 differences between human and gorilla, 10 differences between human and chimp, and 30 differences between gorilla and chimp.

g.  A DNA region from gorilla encodes a 1400 amino acid long protein.  A mRNA from this DNA region is found when one sequences the transcriptome from gorilla stomach lining.  The homologous DNA region in humans and chimps appear to encode an amino acid sequence that is < 100 amino acids, and there is no evidence for that gene being expressed in either of these species.

a. Selection acts against new alleles (against mutations), i.e. purifying selection.  The current protein must be better than alternative forms.

b.

8.  What good is the analysis of ancient DNA?

• Migration & Ancestry:Traces ancient human movements

• Interbreeding: Shows genetic traces of archaic humans (Neanderthals, Denisovans) in modern populations, detailing past interactions

• Disease & Adaptation: Links past genomic changes to environmental or lifestyle shifts, revealing how diseases and adaptations evolved in human populations. 

 Identify two strengths and two limitations of using A. fossils and B. genomic analyses to understand relationships among species and evolutionary history. 

1.paths of migration

genetic targets of selection

insights that are not seen in fossils

estimates of time

estimates of strength of selection

1. Direct physical evidence and timeline: Fossils offer concrete physical evidence of past life forms (e.g., bones, footprints) and help establish an absolute or relative timeline for evolutionary events using geological dating methods.

2. Evidence of extinct species and unique morphology: They preserve the morphology (physical structure) of ancient, extinct organisms, allowing scientists to study features, behaviors, and evolutionary transitions that are not observable in present-day species.

1. Detailed and quantifiable data: Genetic and genomic data offer a vast number of characters (DNA sequences) for comparison, which can resolve fine-scale relationships and fill gaps in evolutionary trees, especially for recent divergences.

2. Insight into molecular evolution and function: Genomics helps understand the molecular basis of adaptation, gene flow, and the timing of divergence through molecular clocks, providing information about processes that are invisible in the fossil record.

2. The fossil record is incomplete

   1. Preservation and identification bias: The record is biased toward organisms with hard parts (bones, shells)

   2. Data availability for ancient species: DNA is a fragile molecule that degrades over time, so it is generally not available for species that lived millions of years ago. This limits the application of genomics to relatively recent evolutionary history, typically the last few hundred thousand years.

   3. Inability to provide direct context for extinct forms: Genomic data alone cannot provide direct physical evidence of extinct species' morphology, environment, or specific behaviors, which are primarily informed by fossils. They also do not provide a physical timeline unless calibrated with fossil evidence. 
      

 Identify four steps that are thought to have been necessary in order for life to form.

1. Nucleotides and amino acids (organic molecules) produced

2. Nucleotides become polymerized (RNA, DNA)

    amino acids become polymerized proteins

3. Polymers enclosed in membranes

4. Membrane-enclosed polymers acquire cellular properties

Two challenges:  

need to concentrate molecules 

    AND 

stabilize polymers