Evolution

• The main components of the learning process are attention, encoding, storage, and retrieval.
• EVOLUTION BY NATURAL SELECTION

  Three conditions:

  • Heritable characters (realising this was not simple!)

  • Characters vary between individuals

  • Differential fitness (= survival, reproduction) between individuals
• Evolution = genetic change over time (strictly speaking, change in allele frequencies) in a population
• Natural selection operates on phenotypes, not genotypes
• speciation = species divide and change
• Natural selection is the only consistent force leading to adaptations
• EVIDENCE FOR EVOLUTION

  • Fossils • Imperfection • Molecular genetics• Natural selection in action

  • Biogeography
• FOSSIL EXAMPLE

  Trilobites disappeared around 250 MYr ago – lived for 280 MYr, showed clear signs of evolutionary change over “short” periods (3 MYr!)

  A)

  
• BAD DESIGN EXAMPLE

  • Left recurrent laryngeal nerve

  • Distance from brain to larynx <30cm

  • Loops round aorta • Around 1m long!
• BIOGEOGRAPHY- OCEANIC ISLANDS

  • Native species: plants, birds, arthropods, often with specific adaptations

  • Species similar to those on nearest land-mass

  • Darwin struck by this on the voyage of The Beagle

  • Modern island biogeography increasingly affected by humans
• BIOGEOGRAPHY- MARSUPIALS

  • Marsupials (pouched mammals) found in Australia and the Americas

  • Marsupials arose in Americas 80 MY ago, arriving in Australia 30 MY ago
• CONVERGENT EVOLUTION: distantly related species show similar adaptations due to similar selection pressures, but often with different underlying genetic factors
• CE: DESERT PLANTS

  • “Succulents” – fleshy stems store water, small leaves reduce water loss, spines deter herbivores

  • Two completely different families:

  Cacti in North and South America

  Euphorbs in “Old World”

  • Not specific local adaptations – both families now present in “wrong” ecosystem due to human intervention

  • Convergent adaptations to life in arid conditions
• CE: TREES

  • Large, long-lived plants with wood and leaves

  • Wood = lignin and cellulose dense tissue

  • Tree-ness has evolved (and disappeared) repeatedly in separate lineages

  • The common ancestor of a nettle and a strawberry was a tree

  • The common ancestor of a maple tree and a mulberry tree was not a tree
• carcinisation: relatives of squat lobsters and hermit crabs that have evolved a crab shape
• EXAMPLES OF CREATED SELECTION

  • Bulbs of green fritillary prized in Chinese medicine

  • Humans harvest bulbs intensively on mountainsides

  • What do you think has happened to the colour of the plant in areas of high harvesting?
• EXAMPLE: LIZARDS

  • Researchers studying lizards on Caribbean island

  • Measured animals, then Hurricane Irma hit

  • They returned a few weeks later and measured population again (NB no reproduction in interval)

  • Average lizard now had bigger toe pads, longer arms, shorter hind legs

  • Suggests animals without these characters tended to die in storm 

  • This shows natural selection, but not evolution (evolution = change in allele frequences in a population)
• MOLECULAR GENETICS

  • DNA is the universal carrier of the genetic code

  • The code is universal

  • Shows existence of a common ancestor

  • Possible to track evolution by comparing genetic sequences directly or by looking at proteins
• MOLECULAR CLOCK

  Pairs of species compared for the same protein – coding differences highly correlated with divergence derived from fossil data. Genetic differences appear to accumulate at a constant rate.
• molecular clock = An evolutionary tree of the cytochrome c gene (found in mitochondria) closely correlates with morphological trees
• Evolution of birds

  *198 species of bird, 259 loci: shows a pattern of evolution (grey nodes = fossils)

  *reaches back to before the demise of non-avian dinosaurs

  *shows a rapid appearance of major groups after extinction

  *speciation = recent evolution of caracara and bowerbirds
• Evolution of whales

  *Cetaceans (whales, porpoises and dolphins) have returned to the water

  *In cetaceans, 68% of OR genes are pseudogenes- non-functional

  -->sea-lion = 37%

  -->dog = 27%

  -->cow = 17%
• Lactase persistence genes show strong evidence of natural selection, but not all genetic sequences can be seen by selection:

  *several different genotypes associated with digesting milk

  *lactase persistence levels highest in Europe and in regions with strong pastoralist traditions

  *people were consuming milk long before the appearance of the relevant alleles

  *appears that advantage came during periods of famine or pathogen exposure
• Natural Theory

  *the genetic code is 'redundant'- some mutations in codons will not change the amino acid ("synonymous changes")

  *many DNA sequences are not genes and apparently have no function ("junk DNA")

  *mutations in these parts of the genome should evolve randomly, as they are selectively "neutral"

  *these non-coding regions provide the best molecular clocks
• Earth, 4 billion years ago

  • Repeated bombardment brings water and destruction

  • Strong young sun, high UV at the surface

  • Darwin’s ‘warm muddy pond’ seems unlikely
• Deep Sea, 3.8 billion years ago

  Energy to fuel first replicating molecules may have come from proton gradients around alkaline hydrothermal vents – this is ‘Lost City’ in mid-Atlantic, where weird bacteria have recently been identified
• Earliest life

  • All DNA life traces back to LUCA – Last Universal Common Ancestor

  • Earliest life probably used RNA as enzymes, which could copy themselves

  • Amino acids can form spontaneously, but they will have been used by life after the RNA world

  • DNA very fragile (RNA even more so) • Needs protection – a cell
• How can you have a cell without DNA?

  • Tiny pores in rocks around vents

  • Lipid “protobionts” can “reproduce” and metabolise...

  • RNA can spontaneously reproduce within them
• Earliest life

  • First prokaryotes were methane-producing bacteria

  • O2 levels remain low (< 0.001% of current levels)

  • Cyanobacteria (aka blue-green algae) produce O2

  • For hundreds of millions of years, this O2 consumed by methanogenic bacteria

  • Most methanogens eventually die out, perhaps due to changes in trace metals in sea
• Eukaryotes

  • Nucleus, mitochondria, chloroplasts (in plants and algae), Golgi bodies, sex, phagocytosis

  • Far outnumbered by prokaryotes (bacteria, archaea)

  • Individual cells up to 1,000,000 times the volume of a prokaryote

  • Some eukaryotes multicellular (most lineages are unicellular)
• Eukaryogenesis

  *Happened once around 2 billion years ago

  *Probably: an archaebacterium engulfed a heterotrophic eubacterium, which eventually became mitochondria

  *The energy provided by mitochondria allows for large, complex life

  2nd event for plants: autotrophic eubacterium engulfed by eukaryotic plant ancestor

  *Not the product of natural selection!

  *In nearly 2 billion years, natural selection did not

  find a way of creating a eukaryote
• Eukaryotes

  *membrane-bound organelles:

  -->nucleus

  -->mitochondria

  *ALSO: large genomes, phagocytosis, meiosis, straight chromosomes, introns etc
• The Cambrian Explosion – 540-515 Myr ago

  • During a relatively short period (20-30 MY) most of the types of animal we now see first appeared (Arthropods, chordates, worms etc)

  • Soft bodies- preservation in Burgess Shale

  Why did it happen?

  • Physiological change – dissolved oxygen levels allow active life-style

  • Geographical change – new seas and new niches

  • Geochemical change – sea-level changes leads to abundance of trace metals to make exoskeletons

  • Biological change – increase in zooplankton allows new predators to arise, increasing selection pressure
• Speciation is a problem to apply to prokaryotes and eukaryotes that are not strictly sexual, such as most plants.
• Speciation is impossible to use with extinct organisms, difficult with bacteria and archaea that have horizontal gene transfer.
• The “biological” definition of a gene is a population of reproducing organisms that is isolated from other populations.
• Speciation

  Species can appear:

  * in time along a lineage, such as humans and chimpanzees,

  *in space due to geographic isolation, such as animals on an island

  *various genetic effects can play a role

  *these can be identified/ detected by comparing populations using population genetics
• Allopatric speciation, the classic and widespread mode of speciation, occurs when different selection pressures and adaptations lead to speciation in two zones.
• Allopatric speciation is exemplified by two different species of antelope squirrels on either side of the Grand Canyon, with birds showing no such effects on either side.
• Genetic drift, a random effect, can cause major changes in small populations.