LS1: Lecture 5

Mon July 8, 2013

Dr. Allison Alvarado, mariposa@ucla.eduOff Hrs: M/W 8:15-8:45 & 11-11:30 Hershey 318

Clinal VariationCLINE (Greek: κλίνω = to possess or exhibit gradient)

It is a gradient of morphological, physiological or genetic change in a group of related organisms usually along a line of environmental or geographic transition (Figure A). Adjacent populations usually can interbreed.

Clines can be produced by 1) previously isolated populations coming into secondary contact and mixing extensively, or 2) they can be the product of divergence in situ along an environmental gradient

What if circumstances made it so the two end populations do meet up (Figure B & C)?

Ring Species: Ensatina

Living examples of “speciation in action”

Ensatina eschscholtzii

Most adjacent populations look similar & mate with one another

Except the two populations at the end of the loop! Here, the two populations

look different and behave as distinct “species” Currently studied by Tom Devitt

Ring Species: Ensatina

Subspecies have new color patterns & adaptations for living in different environments

The two subspecies that meet in Southern California have each evolved so much that they don’t interbred much

Ensatina represents all the gradual changes that accumulate in two lineages and that wind up making “species” incompatible with one another

Ring Species

What about Ensatina's evolutionary future?

In a few locations in Southern California where the muted western form (eschscholtzii) and the blotchy eastern form (klauberi) live together, they actually do occasionally interbreed, producing blurrily blotched hybrids

Why do the two forms interbreed in some places and not others???

Since they can interbreed, what's keeping the two forms distinct???

Why don't these two subspecies blend into one another, as the forms around the rest of the ring do???

Ring Species

Why don’t eschscholtzii and klauberi interbreed more than they do?

Hypothesis A: They rarely recognize each other as potential mates, because of differences in smell (e.g., a pheromone), a physical trait (e.g., a color pattern), or a behavior (e.g., a particular mating call or dance)

Hypothesis B: They rarely mate because they rarely meet. For example, the two might prefer different habitats, such that they rarely run into one another, let alone get together an interbreed.

Or, some combination of these factors might come into play…

Ring Species: Phylloscopus trochiloides In central Siberia, two distinct forms of

greenish warbler (P. t. viridanus in blue and P. t. plumbeitarsus in red) coexist (potentially without interbreeding). Therefore these two forms may be considered distinct species.

What’s interesting is that the two forms are connected by a long chain of populations/subspecies encircling the Tibetan Plateau to the south.

Traits (e.g.wing bar & song) change gradually through this ring of populations.

The idea is they originated from a single population in the south (e.g. yellow). As they expanded northward along east and west sides of the mountains, they gradually diverged, accumulating differences until they finally met in the north.

Ring Species: Song Variation

Playback studies/experiments show a male will aggressively respond to songs that it recognizes as belonging to its own “species” (e.g. blue vs. blue) but it usually will not respond to song from a distantly related population (e.g. blue vs. red).

Females probably also use the song differences to distinguish among potential mates.

If males and females from the different subspecies (i.e. red vs. blue) do not mate, then they are reproductively isolated & considered separate species under the biological species concept!

As stated in previous slide, songs differ distinctly between viridanus (blue) and plumbeitarsus (red) but change gradually around the southern side of the ring. Songs are simple in the south and become more complex northward, in two distinct ways.

Evolutionary Relationships In biology we must consider profound changes in the nature of life on

Earth over immense periods of time.

There are two major analytical tools that biologists use to reconstruct the history of life: phylogenetic trees and the fossil record. Phylogenetic trees document the evolutionary relationships among

organisms and are estimated from data. The fossil record provides physical evidence of organisms that lived in

the past.

Distinguishing Homology from Homoplasy

Problems can arise because similar traits can evolve independently in two distant species rather than from a trait present in a common ancestor.

Homology occurs when traits are similar due to shared ancestry.

Homoplasy occurs when traits are similar for reasons other than common ancestry. For example, ichthyosaurs (extinct aquatic reptiles) and dolphins (extant mammals)

are very similar, but these similarities are not due to common ancestry.

Distinguishing Homology from Homoplasy

Convergent evolution occurs when natural selection favors similar solutions to the problems posed by a similar way of life.

Convergent evolution is a common cause of homoplasy.

If similar traits found in distantly related lineages are indeed similar due to common ancestry, then similar traits should be found in many intervening lineages on the tree of life.

Distinguishing Homology from Homoplasy

Parsimony is a principle of logic stating that the most likely explanation or pattern is the one that implies the least amount of change.

Convergent evolution and other causes of homoplasy should be rare compared with similarity due to shared descent

The tree that implies the fewest overall evolutionary changes should be the one that most accurately reflects what happened during evolution.

Tools for Studying History: The Fossil Record

A fossil is the physical trace left by an organism that lived in the past.

The fossil record provides the only direct evidence about what organisms that lived in the past looked like, where they lived, and when they existed.

How Do Fossils Form?

Fossilization preserves traces of organisms that lived in the past.

Most of the processes that form fossils begin when part or all of an organism is buried in ash, sand, mud, or some other type of sediment.

Preservation after Burial There are four main types of fossils:

1. Intact fossils form when decomposition does not occur.

2. Compression fossils form when sediments accumulate on top of the material and compress it into a thin film.

3. Cast fossils form when the remains decompose after burial and dissolved minerals create a cast in the remaining hole.

4. Permineralized fossils form when the remains rot extremely slowly and dissolved minerals infiltrate the interior of the cells and harden into stone.

Fossilization Is a Rare EventFossilization only occurs under ideal conditions.

There are 10 specimens of the first bird to appear in the fossil record, Archaeopteryx.

As far as researchers currently know, only 1 out of every 200,000,000 individuals fossilized.

Limitations of the Fossil Record

Paleontologists—scientists who study fossils— recognize that there are several limitations of the fossil record:

1. Habitat bias occurs because organisms that live in areas where sediments are actively being deposited are more likely to fossilize than are organisms that live in other habitats.

2. Taxonomic bias is due to the fact that some organisms (e.g., those with bones) are more likely to decay slowly and leave fossil evidence.

3. Temporal bias occurs because more recent fossils are more common than ancient fossils.

4. Abundance bias occurs because organisms that are abundant, widespread, and present on Earth for a long time leave evidence much more often than do species that are rare, local, or ephemeral.

Adaptive RadiationsAdaptive radiations (when rapid

speciation in a single lineage is followed by divergence into many different adaptive forms) are a major pattern in the history of life. They are instances of rapid diversification associated with new ecological opportunities and new morphological innovations.

Biologists use the term NICHE to describe the range of resources that a species can use and the range of conditions that it can tolerate. Hawaiian honey creepers and silverswords occupy a wide array of niches.

The Hawaiian silverswords fulfill the three hallmarks of an adaptive radiation: They are a monophyletic group.They speciated rapidly.They diversified ecologically.

Ecological Opportunity as a Trigger One of the most consistent triggers of adaptive radiations is ecological

opportunity—the availability of new types of resources.

For example, biologists have documented adaptive radiations of the Anolis lizards of the Caribbean islands.

On the two islands studied, the same four ecological types eventually evolved, because the islands had similar varieties of habitats. Therefore, similar adaptive radiations took place independently on the two islands, triggered by the available environment and lack of competition.

Morphological Innovation as a Trigger

Morphological innovation can also be a trigger for adaptive radiation.

Many of the other important diversification events in the history of life started off with the evolution of a key morphological trait that allowed descendants to live in new areas, exploit new food sources, or move in new ways.

Examples of Morphological Innovations

The evolution of wings, three pairs of legs, complex mouthparts, and a strong external skeleton helped insects move and feed efficiently. Today insects are the most diverse lineage on Earth, with perhaps well over 3 million species in existence.

Flowers are a unique reproductive structure that are particularly efficient at attracting pollinators, making angiosperms (flowering plants) more reproductively efficient. Today angiosperms are far and away the most species-rich lineage of land plants. Over 250,000 species are known.

Examples of Morphological Innovations

Cichlids are a lineage of fish that evolved a unique set of jaws in their throat, making food processing extremely efficient. Different species have throat jaws specialized for feeding on different foods. Over 300 species of cichlid live in Africa’s Lake Victoria alone.

Feathers and wings gave some dinosaurs the ability to fly. Today the lineage called birds contains about 10,000 species, with representatives that live in virtually every habitat on the planet.

Anolis lizardsEach ecomorph on the different islands is not the same species

Homology or homoplasy?

Different lizard species colonized different islands, so each ecomorph is an example of convergent evolution

Whale Evolution: A Case History

Traditionally, phylogenetic trees based on morphological data place whales as the outgroup (a species or group that is closely related to the monophyletic group but not part of it)

Whale Evolution: A Case History

DNA sequence data, however, suggest a close relationship between whales and hippos. This tree would require two changes to the astragalus trait.

Life's TimelineEarth started to form about 4.6

billion years ago, and that life began around 3.4 billion years ago.

Divide Earth history into segments called eons, eras, and periods.

Radiometric dating allows assignment of absolute dates, expressed as years before the present, to events in the fossil record.

The PrecambrianThe Precambrian encompasses

the Hadean, Archaean, and Proterozoic eons.

This period spans from the formation of the Earth to the appearance of most animal groups about 542 million years ago (mya).

In the Precambrian era, almost all life was unicellular and hardly any oxygen was present.

The Phanerozoic EonThe Phanerozoic eon spans the interval between 542 mya and the

present. It is divided into three eras—the Paleozoic, the Mesozoic, and the Cenozoic—that are further divided into periods.

The Phanerozoic Eon The Cenozoic era (Age of Mammals) includes the interval from 65.5 mya to the present. During this time the mammals diversified

after the disappearance of the dinosaurs.

The Mesozoic era (Age of Reptiles) covers the interval from 251 to 65.5 mya. This era saw the rise and dominance of the

dinosaurs and ended with their extinction.

The Paleozoic era covers the interval from 542 to 251 mya. Many groups—including fungi, land plants,

and land animals—1st appeared.You should be able to put the following events in the correct order:

a. first land plantsb. first reptilesc. first amphibiansd. first angiospermse. first beesf. first horsesg. first birds

The Cambrian Explosion

The first animals appear in the fossil record around 565 mya, at the end of the Proterozoic eon.

Soon after that in geologic time, by about 50 million years later, animals had diversified into almost all the major groups living today.

This diversification is known as the Cambrian explosion. What triggered it? Increased oxygen levels is one hypothesis.

This period saw what was arguably the most evolutionary change in the history of life.

The three domains Bacteria and Archaea form two of the three largest branches on the tree

of life. The third major branch or domain is Eukarya, the eukaryotes.

Virtually all members of the bacteria and archaea are unicellular and all are prokaryotic (lacking a membrane-bound nucleus).

Bacteria and archaea are distinguished by the types of molecules that make up their plasma membranes and cell walls, and by the machinery they use to transcribe DNA and translate mRNA into proteins.

Comparisons between Bacteria and Archaea

1. Cell walls

Bacteria - peptidoglycan

Archaea - unique polysaccharides

2. Plasma membranes

Bacteria - similar to eukaryotes

Archaea - unique plasma membranes

3. Ribosomes

Bacteria - ribosomes and RNA polymerase are distinct

Archaea - similar to eukaryotes

Study techniquesEnrichment Cultures

Growing strains in the lab to generate enough individuals for study

Direct SequencingWay to study molecular diversity in forms that can’t be grown in

an enrichment culture, enables us to determine the habitat and phylogeny of many new lineages

Comparing molecular phylogenies

Evaluating Molecular Phylogenies

Some of the most useful phylogenetic trees for domains Bacteria and Archaea have been based on studies of ribosomal RNA (rRNA) found in the small subunit of ribosomes.

In the late 1960s Carl Woese and colleagues determined and compared the 16S and 18S RNA molecules from a wide array of species.

The Universal TreeThis revised tree of life

shows that domain Bacteria was the first lineage to diverge from the common ancestor of all living organisms.

It also shows that the Archaea and Eukarya are more closely related to each other than they are to the Bacteria.

Why do scientists want to learn more about these domains?

Although we don’t see them with the naked eye, it’s obvious that Bacteria and Archaea are important in our everyday lives

We are learning more about these organisms than any other group today, and our knowledge of this group is increasing at a rapid rate

How important are these prokaryotic domains?

Bacteria and archaea may be tiny, but they are ancient, diverse, abundant, and ubiquitous.

Biologists estimate the total number of individual bacteria and archaea alive today at 5 1030

They live in virtually every habitat known and use remarkably diverse types of compounds in cellular respiration and fermentation.

Although cell size is usually small and overall morphology is relatively simple, the chemistry they can do is extremely sophisticated.

Some Bacteria Cause DiseaseAn infectious disease is one spread by being passed from an

infected individual to an uninfected individual.

The experiments of Robert Koch in the late 1800s became the basis for the germ theory of disease.

In industrialized countries, improvements in sanitation and nutrition have dramatically reduced mortality rates due to infectious diseases since 1900.Most of the decline in deaths

due to infectious diseases occurred before the introduction of antibiotics!

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Penicillin, the first widelyavailable antibiotic, wasinitially used here

The Past, Present, and Future of Antibiotics

The discovery of antibiotics (molecules that kill bacteria) in 1928 and their widespread use starting in the 1940s allowed physicians to effectively combat most bacterial infections.

However, overuse of antibiotics since the late twentieth century has lead to antibiotic-resistant strains of bacteria.

What Makes Some Bacterial Cells Pathogenic?

Virulence, or the ability to cause disease, is a heritable trait that varies among individuals in a population.

Some species have both pathogenic virulent strains and harmless strains. In Escherichia coli, for example, the virulence of the strain

depends upon the length of the genome and the toxicity of the resulting proteins.

The Biological Impact of Bacteria and Archaea

Only 5000 species of bacteria and archaea have been named and described, but biologists are virtually certain that millions exist. Over 400 species live in the human digestive

tract. About 128 species live in the lining of the

human stomach. Approximately 500 species live in the human

mouth.

Microbiology is the study of microbes, microscopic organisms.

Many bacteria are “good”

Bacteria play a key role in ecosystems:Photosynthetic bacteria were responsible for the increase of the

oxygen atmosphereBacteria (and archaea) cycle nutrients through terrestrial and

aquatic environmentsSome bacteria (and archaea) are even effective at cleaning up

pollution

Bioremediation

Some of the most serious pollutants in soils, rivers, and ponds consist of organic solvents or fuels that leaked or were spilled into the environment.

These pollutants are toxic, do not dissolve in water, and accumulate in sediments.

Bioremediation is the use of bacteria (and archaea) to degrade pollutants.

BioremediationBioremediation uses two complementary strategies:

1. Fertilizing contaminated sites to encourage the growth of existing bacteria (and archaea) that degrade toxic compounds.

2. “Seeding,” or adding, specific species of bacteria (and archaea) to contaminated sites.

The Habitat Diversity of Prokaryotes

Bacteria and archaea live almost everywhere, from below the Earth’s surface to on Antarctic sea ice.10 percent of the world’s

biomass may be comprised of prokaryotes living under the ocean.

Bacteria and archaea have been found at depths of 10,000 m, and in temperatures ranging from 0° to 121°C.

Extremophiles

Extremophiles: bacteria (or archaea) that live in high-salt, high-temperature, low-temperature, or high-pressure habitats

“Hot” area of research for several reasons:

1. Understanding extremophiles may help explain how life on Earth began.

2. Astrobiologists use extremophiles as model organisms in the search for extraterrestrial life.

3. Enzymes that function at extreme temperatures and pressures are useful in industrial processes, such as the use of Taq polymerase in PCR.

Evolutionary Themes The oldest fossils found thus

far are of 3.5-billion-year-old prokaryotes. Eukaryotes do not appear in the fossil record until 1.7 billion years later.

What helps biologists make sense of the diversity observed among these organisms?

Morphologic and metabolic characters provide most of the information used for categorizing bacterial species

Morphological DiversityBacteria and archaea show extensive morphological diversity

in terms of size, shape, and motility.The volume of bacterial species ranges from 0.15 m3 to 200 x

106 m3.

Bacteria range in shape from filaments, spheres, rods, and chains to spirals.

Bacteria have a range of modes of motility.

BacteriaSome were recognized by distinctive morphological

characteristics, others by phylogenetic analyses of gene sequence data

Bacteria are a monophyletic group. Within this group there are at least 16 major lineages; the six in your book are Firmicutes, Spirochaetes, Actinobacteria, Chlamydiae, Cyanobacteria, & Proteobacteria