Evolution Resources

[EvoResources]

Evolution Resources

This thread is a guide to sites that are either dedicated to evolution or have a significant area devoted to the subject. I have tried to stick to what can be recognised as reputable organisations. Sites for a younger audience are often mixed in with teaching resources so they are all there together. This is not a discussion thread on so I have locked the topic. If you want to make suggestions or comments please do so here.

For books on evolution please browse and post in The Book Nook where there are a number of threads already running on this subject.

Thanks
CJ

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Guides
Frequently asked questions about evolution What is evolution? Biological evolution refers to the cumulative changes that occur in a population over time. These changes are produced at the genetic level as organisms' genes mutate and/or recombine in different ways during reproduction and are passed on to future generations. Sometimes, individuals inherit new characteristics that give them a survival and reproductive advantage in their local environments; these characteristics tend to increase in frequency in the population, while those that are disadvantageous decrease in frequency. This process of differential survival and reproduction is known as natural selection. Non-genetic changes that occur during an organism's life span, such as increases in muscle mass due to exercise and diet, cannot be passed on to the next generation and are not examples of evolution.

Understanding Evolution, University of California Understanding Evolution is a non-commercial, education website, teaching the science and history of evolutionary biology. This site is here to help you understand what evolution is, how it works, how it factors into your life, how research in evolutionary biology is performed, and how ideas in this area have changed over time.

Howard Hughes Medical Institute 2005 holiday lectures. 4 hours of video on various aspects of evolution, including a fascinating introduction to Charles Darwin; both his work and his life.

The Talk Origins Archive is a collection of articles and essays, most of which have appeared in talk.origins at one time or another. The primary reason for this archive's existence is to provide mainstream scientific responses to the many frequently asked questions (FAQs) that appear in the talk.origins newsgroup and the frequently rebutted assertions of those advocating intelligent design or other creationist pseudosciences.

PBS Wide selection of videos, very accessible, including one about the evolution of the eye.

The complete works of Charles Darwin This website is the largest collection of writings by and about Darwin ever published. It contains his complete publications, thousands of handwritten manuscripts and the largest Darwin bibliography and manuscript catalogue. There are also over 200 supplementary texts, from reference works, reviews, obituaries, biographies and more.

Darwiniana and Evolution Darwiniana.org is a resource for anyone interested in evolution. It contains information on fossils, genetics, evolutionary theory, botany, zoology, creationism and ID. Extensive links to other reliable sites are provided. It even has a picture of A. R. Wallace. Who was Wallace? Go have a look.

Evolution Timeline The timeline of human evolution outlines the major events in the development of human species, and the evolution of humans' ancestors. It includes a brief explanation of some animals, species or genus, which are possible ancestors of Homo sapiens sapiens. It begins with the origin of life and presents a possible line of descendants that led to humans

Interactive Time Line Very informative interactive time line going back to the Big Bang. It takes a few seconds to load. Unless your screen is quite wide you can't see the right hand end of the line which is our bit.

Evolution and the Fossil Record This non-technical introduction to evolution, produced by the American Geological Institute in cooperation with the Paleontological Society, aims to help the general public gain a better understanding of one of the fundamental underlying concepts of modern science. Also has a 36 page booklet.

Tree of Life Web Project The Tree of Life Web Project (ToL) is a collaborative effort of biologists from around the world. On more than 9000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics.

Becoming Human Organisation The Institute of Human Origins (IHO) conducts, interprets and publicizes scientific research on the human career. IHO's unique approach brings together scientists from diverse disciplines to develop integrated, bio-behavioural investigations of human evolution. Through research, education, and the sponsorship of scholarly interaction, IHO advances scientific understanding of our origins and its contemporary relevance. Combining interdisciplinary expertise and targeted funding, IHO fosters the pursuit of integrated solutions to the most important questions regarding the course, cause and timing of events in human evolution.

New Evolution: 24 myths and misconceptions So here is New Scientist's guide to some of the most common myths and misconceptions about evolution.

Academic Sites and Guides
The Society for the Study of Evolution Subscription site for serious study. The Society for the Study of Evolution was founded in March, 1946. The objectives of the Society for the Study of Evolution are the promotion of the study of organic evolution and the integration of the various fields of science concerned with evolution. The Society publishes the scientific journal Evolution and holds annual meetings in which scientific findings on evolutionary biology are presented and discussed.

Evolutionary Psychology Evolutionary Psychology is an open-access peer-reviewed journal that aims to foster communication between experimental and theoretical work on the one hand and historical, conceptual and interdisciplinary writings across the whole range of the biological and human sciences on the other.

The Paleobiology Database is an international scientific organization run by paleontological researchers from many institutions. We are bringing together taxonomic and distributional information about the entire fossil record of plants and animals. Our goal is to educate the public, summarize the literature for professionals, and foster statistical analyses of mass extinctions and other aspects of biodiversity. Note: you must register and have a scientific interest in the core data there are some publicly accessible elements.

New Scientist Another vast site with lots of recent developments from New Scientist magazine.[/quote]

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Museums

NEW the Human Origins Initiative Smithsonian National Museum of Natural History. A new exhibition hall dedicated to the discovery and understanding of human origins will open next year at the Smithsonian’s National Museum of Natural History. Based on decades of cutting-edge research by Smithsonian scientists, the David H. Koch (pronounced “coke”) Hall of Human Origins will premiere March 17, 2010, which also marks the 100-year anniversary of the museum’s official opening on the National Mall.

The Virtual Fossil Museum Fossils across geological time presented in multiple contexts of geological history, the tree of life, paleobiology and evolution. The Virtual Fossil Museum is an educational resource providing an ever-growing extensive collection of fossil images.

London's Natural History Museum Welcome to the Natural History Museum. We promote the discovery, understanding, enjoyment, and responsible use of the natural world. Explore our world-class collections, fantastic exhibitions and cutting-edge research online, or visit our landmark buildings.

Natural History Museum at Tring Discover the fascinating range of animals collected by Lionel Walter Rothschild in our beautiful Victorian Museum. It is home to the world-class research and collections of the Natural History Museum's Bird Group.

University of Nebraska State Museum Explore Evolution is a major new partnership forged between science museums and 4-H organizations to bring current research on evolution to the public. The project features the work of scientists who are making leading discoveries about the evolution of life. From rapidly evolving HIV to whales that walked, the public is invited to explore evolution in organisms ranging from the very smallest to the largest.

The Field Museum of Natural History, Chicago Discover the man and the revolutionary theory that changed the world in Darwin. Exhibition runs June 15, 2007 - January 1, 2008.

Teaching guides, education resources and kids/teenager guides
Access Excellence Education Resources The National Health Museum

Evolution and the Nature of Science The National Academies Press

Evolution Resources From the National Academies This Web page is designed to provide easy access to books, position statements, and additional resources on evolution education and research. These materials have been produced by the National Academies and other sources.

National Center for Science Education The National Center for Science Education (NCSE) defends the teaching of evolution in public schools. We are a nationally-recognized clearinghouse for information and advice to keep evolution in the science classroom and "scientific creationism" out. NCSE is the only national organization to specialize in this issue.

Swathmore College Evolution resources for the public school teacher

Welcome Trust Big Picture on Evolution
"Nothing in biology makes sense except in the light of evolution." Theodosius Dobzhansky (1973)

The Evolution Report, hosted by Paul Wilson The Evolution Report is a series of audio programs on evolutionary topics. It is primarily intended to be supplemental instruction for BIOL 322 Evolutionary Biology. Students say that they don't have enough time to study more than they are already studying, but many spend tons of down-time in their cars and relaxing before bed. Our idea then was to produce an entertaining show that could be listened to during this down-time and that would not consume high-quality time. The goal is to make evolutionary topics more familiar.

Miscellaneous
Evolution, a philosophical perspective Stanford Encyclopaedia of Philosophy

Darwin Day Darwin's 200th Birthday will occur on February 12, 2009; it will also be the 150th Anniversary of the publication of his famous book, On The Origin of Species. So, together we can evolve a truly international Celebration to express gratitude for the enormous benefits that scientific knowledge, acquired through human curiosity and ingenuity, has contributed to the advancement of humanity.

Member Sites
Understanding Evolution: History, Theory, Evidence, and Implications An astonishingly extensive site with a great breadth of information. Warning there are a number of very explicit images of deformed foetuses towards the end of the site. Also available in hard copy here.

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Blogs, wikis and forums

By the nature of blogs there will be all sorts of things here so dive in and have a look.

The Panda's Thumb is the virtual pub of the University of Ediacara. The patrons gather to discuss evolutionary theory, critique the claims of the antievolution movement, defend the integrity of both science and science education, and share good conversation.

Pharyngula is the blog of PZ Myers a biologist and associate professor at the University of Minnesota. Evolution, development, and random biological ejaculations from a godless liberal!

Darwin Central is concerned with the theory of evolution as a scientific topic. We do not concern ourselves with either religious objections to the theory or with political objections based on the theory's alleged social consequences. We recognize that some denominations which follow a literal interpretation of scripture object to biological evolution because they feel it conflicts with their interpretation of scripture. There are other denominations that do not share this view. The NCSE's collection of Statements from Religious Organizations consists of a list of Christian and Jewish denominations, including the Roman Catholic Church, that accept (or at least do not dispute) evolution. There is also the recent statement opposing creationism by the Archbishop of Canterbury, leader of the 70-million-member Anglican Communion. We have no desire to participate in such inter-denominational disputes.

List-o-links Maintained since 1999 this list dwarfs anything else I've seen. So after you've had your fill here there's plenty more to be found on this link. Plenty of stuff to shoot down creationists with as well.

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Specific Examples

Some people wish to refute or deny evolution exists or has ever happened and demand examples as proof. These links are hard scientific evidence of evolution, if somebody felt that they had a good case to refute evolution they would have to categorically disprove these examples in open scientific debate. They are provided for information. If you have any original source material of this nature please send the details to me in a PM.

Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish
Abstract. Freezing avoidance conferred by different types of antifreeze proteins in various polar and subpolar fishes represents a remarkable example of cold adaptation, but how these unique proteins arose is unknown. We have found that the antifreeze glycoproteins (AFGPs) of the predominant Antarctic fish taxon, the notothenioids, evolved from a pancreatic trypsinogen. We have determined the likely evolutionary process by which this occurred through characterization and analyses of notothenioid AFGP and trypsinogen genes. The primordial AFGP gene apparently arose through recruitment of the 5 and 3 ends of an ancestral trypsinogen gene, which provided the secretory signal and the 3 untranslated region, respectively, plus de novo amplification of a 9-nt Thr-Ala-Ala coding element from the trypsinogen progenitor to create a new protein coding region for the repetitive tripeptide backbone of the antifreeze protein. The small sequence divergence (4-7%) between notothenioid AFGP and trypsinogen genes indicates that the transformation of the proteinase gene into the novel ice-binding protein gene occurred quite recently, about 5-14 million years ago (mya), which is highly consistent with the estimated times of the freezing of the Antarctic Ocean at 10-14 mya, and of the main phyletic divergence of the AFGP-bearing notothenioid families at 7-15 mya. The notothenioid trypsinogen to AFGP conversion is the first clear example of how an old protein gene spawned a new gene for an entirely new protein with a new function. It also represents a rare instance in which protein evolution, organismal adaptation, and environmental conditions can be linked directly.

29+ Evidences for Macroevolution
Abstract. According to the theory of common descent, modern living organisms, with all their incredible differences, are the progeny of one single species in the distant past. In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all life. Some of the macroscopic properties that characterize all of life are (1) replication, (2) heritability (characteristics of descendents are correlated with those of ancestors), (3) catalysis, and (4) energy utilization (metabolism). At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree.

If every living species descended from an original species that had these four obligate functions, then all living species today should necessarily have these functions (a somewhat trivial conclusion). Most importantly, however, all modern species should have inherited the structures that perform these functions. Thus, a basic prediction of the genealogical relatedness of all life, combined with the constraint of gradualism, is that organisms should be very similar in the particular mechanisms and structures that execute these four basic life processes.

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YouTube videos and the like

Origin of Life.
A lecture by John Maynard Smith that goes right to the heart of the development of DNA and consequently life and not life. WATCH THESE! Part 1 Part 2 Part 3 Part 4 Part 5 Part 6

Darwin's Dangerous Idea 1/11 2/11 3/11 4/11 5/11 6/11 7/11 8/11 9/11 10/11 11/11

A selection of excellent videos suggested by Basilio720
History of the Universe Made Easy (Part 1)
History of the Universe Made Easy (Part 2)
The Origin of Life made easy
God and DNA made easy

Suggestions? please drop me a PM or add to this topic please.

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Related sites of interest

These sites are usually biology based and give insights into the evolutionary process while not being specifically about evolution.

Digital Morphology The Digital Morphology library is a dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens. Browse through the site and see spectacular imagery and animations and details on the morphology of many representatives of the Earth's biota.

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Our own topics worth following.

Why no evolving? response by Just A Theory here.
Gene sequence Fallacies by Calilasseia
Serial Trials Fallacy by Calilasseia


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Links to some interesting threads here, added in no particular order.

Revealing the evolutionary history of threatened sea turtles
Scientists propose the creation of a new type of seed bank
Despite 'peacenik' reputation, bonobos hunt/eat primates

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Sticky questions tackled in gecko research
World's oldest fossil impression of a flying insect
Being altruistic may make you attractive
Unique fossils capture 'Cambrian Migration'
Migratory moths hitch their rides, but they're not drifters
Molecular origin of proportional development traced
Brainy genes, not brawn, key to success on mussel beach
Short RNAs show a long history
Bold traveller's journey toward the center of the Earth
Serendipitous discovery reveals earthworms more diverse
Digital zebrafish embryo offers 1st complete devo blueprint
How infectious bacteria can switch species
Researchers document world's mammals in crisis
Swarms follow high-speed 'streaker' bees to find new nest
Why your boss is white, middle-class and a show-off
How spittlebugs jump
Beetles get by with a little help from their friends
'Sandfish' could help materials handling, process technology
Shift in bald eagle diet linked to sea otter decline
Singing to females makes male birds' brains happy
Egalitarian revolution in the Pleistocene?
Gene expression in alligators suggests birds have 'thumbs'
A new dinosaur species, Pachyrhinosaur lakustai, unveiled
Odor attraction among different wildtype Drosophila
Study reveals an oily diet for subsurface life

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Financial risk-taking associated with higher testosterone
Strong leaders who punish cheats can benefit society
America's smallest dinosaur uncovered
Formula discovered for longer plant life
Insight into the evolution of parasitism
Study finds animal with ability to survive climate change
Car fronts at face value
Study shows effect of climate change on animal diversity
Fantastic photographs of fluorescent fish
Luck gave dinosaurs their edge
Research pushes back crop development 10,000 years
Walnut Trees Emit Aspirin-Like Chemical to Deal With Stress
Bats pick up rustling sounds against background noise
'Redesigned hammer' forged evolution of mammal pregnancy
A New Pacific Iguana and More Clues to a Longtime Mystery
Neighbors from hell: Infanticide rife in guillemot colony
Cyanobacterium sequenced features rare linear chromosome
Oil palm plantations no substitute for tropical rainforests
Dominant male deer have the deepest calls
In spiders, size matters: Small males are more often meals
TED: Underwater Astonishments
How corals adapt to day and night
Flies, too, feel the influence of their peers
Stanford DNA study reveals evolution of beer yeasts
Computational biochemist uncovers molecular clue

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Individuals vary immune response according to age, sex, cost
Altenberg! The Woodstock of Evolution?
Synthetic Life Comes One Step Closer
Scavenger birds chew the fat
As Andean glacier retreats, tiny life forms swiftly move in
Lightweight and long-legged males go the distance for sex
Viral contribution to Evolution
Molecular evolution is echoed in bat ears
Study of islands reveals surprising extinction result
Old sheep raising the baaa
Exploding chromosomes fuel research about evolution
Researchers map first plant-parasitic nematode genome
A tiny ancestral remnant lends developmental edge to humans
Clever magpies!
Research challenges assumptions of flightless bird evolution
Trichoplax genome sequenced, evolution's 'rosetta stone'
Graduate student's paper sheds light on bonobo language
How 'secondary' sex characters can drive origin of species
Diversity among parasitic wasps even greater than suspected
"Armoured" Fish Study Helps Strengthen Darwin's Theory
New giant clam species offers window into human past
Ancient mother spawns new insight on reptile reproduction
Jamaican lizards' shows of strength mark territory
Animals adapt their vocal signals to social situations
Genetics reveals big fish that almost got away

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Tahitian vanilla originated in Maya forests
UQ research touches a nerve
Recipe for saving the world's oceans from extinction crisis
Phylogenomic Study of Birds Reveals Evolutionary History
Novel fungus helps beetles to digest hard wood
Genes & nutrition influence caste in unusual harvester ant
Molecular sleuths track evolution through the ribosome
Fish cancer gene linked to pigment that attracts mates
Virophages - Viruses infecting viruses.
Team shows how DNA repairs may reshape the genome
Smells like bees’ spirit
Researchers see history of life in structure of transfer RNA
Sky islands: metaphor or misnomer?
Dying frogs sign of a biodiversity crisis
New dinosaur fossil found.
Why men really do prefer blondes

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Ardipithecus Ramidus

All things Ardi



Discovering Ardi website

Timeline and skeleton at National Geographic

Ardipithecus Ramidus - An Ancient Human Ancestor Surprise - Images and links to the dig site

First of 10 videos "Discovering Ardi"


Full playlist at YouTube

A round table discussion about Ardi

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3 of 5


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5 of 5


Ardipithecus (Article: 'Did apes descend from us?')

Ardipithecus FAQ
Today is Ardipithecus day. Eleven papers in tomorrow’s issue of Science describe the research on one exceptional skeleton (numbered ARA-VP-6/500, nicknamed “Ardi”) as well as more than thirty other individuals, mostly represented by isolated teeth with a few partial sets of teeth.

Ethiopian desert yields oldest hominid skeleton
BERKELEY — Nearly 17 years after plucking the fossilized tooth of a new human ancestor from a pebbly desert in Ethiopia, an international team of scientists today (Thursday, Oct. 1) announced their reconstruction of a partial skeleton of the hominid, Ardipithecus ramidus, which they say revolutionizes our understanding of the earliest phase of human evolution.

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These are free online tasters of Open University courses that provide some simple insights into the subjects they cover. Ideal for those totally new to the subjects. These are the units relevant to evolution but the whole list can be found here

An elegantly simple introduction to Evolution through natural selection

Although aimed at health care this session, Inheritance of characters, gives an introduction to human genetics and their relation to inheritance.

Life in the Palaeozoic does what it says on the tin! Taken from the course S193; Fossils and the History of Life.

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A rolling list of articles about fossil finds, and/or their interpretation, that have appeared in the news and scientific articles. The forum only allows 25 links in a post so once this limit has been reached the oldest link will leave in a FIFO style. Each link is followed by the introduction of the linked article.

The Oldest European Marsupial In Southwest France
ScienceDaily (Nov. 9, 2009) — Remains of one of the oldest known marsupials have been recovered in Charente-Maritime by a palaeontologist team from the Muséum national d'Histoire naturelle (CNRS) and the University of Rennes 1. This discovery raises a new hypothesis about the dispersal route of the earliest marsupial mammals.

Fossil Plant Links Patagonia To New Guinea
ScienceDaily (Nov. 10, 2009) — Fossil plants are windows to the past, providing us with clues as to what our planet looked like millions of years ago. Not only do fossils tell us which species were present before human-recorded history, but they can provide information about the climate and how and when lineages may have dispersed around the world. Identifying fossil plants can be tricky, however, when plant organs fail to be preserved or when only a few sparse parts can be found.

Missing Saurapod Link
Researchers have discovered a fossil skeleton that appears to link the earliest dinosaurs with the large plant-eating sauropods.

Young Tyrannosaurs Did Serious Battle Against Each Other
We all know adolescents get testy from time to time. Thank goodness we don't have young tyrannosaurs running around the neighbourhood.

Neandertals / Neanderthals
A reexamination of ancient human bones from Romania reveals more evidence that humans and Neandertals interbred.

Snail Fossils Suggest Semiarid Eastern Canary Islands Were Wetter 50,000 Years Ago
Fossil land snail shells found in ancient soils on the subtropical eastern Canary Islands show that the Spanish archipelago off the northwest coast of Africa has become progressively drier over the past 50,000 years.

New Analyses Of Dinosaur Growth May Wipe Out One-third Of Species
Palaeontologists from the University of California, Berkeley, and the Museum of the Rockies have wiped out two species of dome-headed dinosaur, one of them named three years ago -- with great fanfare -- after Hogwarts, the school attended by Harry Potter.

Newly Discovered Ankylosaur Dinosaur Is 'Biological Version Of An Army Tank'
A husband and wife team of American palaeontologists has discovered a new species of dinosaur that lived 112 million years ago during the early Cretaceous of central Montana.

Evolution and the Fossil Record
Link to a 36 page .pdf document produced by the American Geological Institute and The Paleontological Society. Very well worth a read. Web page version.
Evolution is one of the fundamental underlying concepts of modern science. This powerful theory explains such phenomena as the history of life preserved in the fossil record; the genetic, molecular, and physical similarities and differences among organisms; and the geographic distribution of organisms today and in the past. Indeed, evolution forms the foundation of modern biology and paleontology and is well documented by evidence from a variety of scientific disciplines.

Largest Pliosaur Skull Found
The fossilised skull of a colossal "sea monster" has been unearthed along the UK's Jurassic Coast.

Geologist Analyzes Earliest Shell-covered Fossil Animals
The fossil remains of some of the first animals with shells, ocean-dwelling creatures that measure a few centimeters in length and date to about 520 million years ago, provide a window on evolution at this time, according to scientists. Their research indicates that these animals were larger than previously thought.

New Type Of Flying Reptile: Darwin's Pterodactyl Preyed On Flying Dinosaurs
An international group of researchers from the University of Leicester (UK), and the Geological Institute, Beijing (China) has identified a new type of flying reptile, providing the first clear evidence of an unusual and controversial type of evolution.

Avian origins: new analysis confirms ancient beginnings
ANN ARBOR, Mich.—Did modern birds originate around the time of the dinosaurs' demise, or have they been around far longer?

In Mammals, a Complex Journey to the Middle Ear
Imagine what a dinner conversation would be like if you had decent table manners, but the ears of a lizard. Not only would you have to stop eating whenever you wanted to speak, but, because parts of your ears are now attached to your jaw, you’d have to stop eating whenever you wanted to hear anybody else, as well. With no fork action on your end, your waiter would soon conclude that you were obviously “done working on that” and would whisk your unbreached baked ziti away.

Trackway Analysis Shows How Dinosaurs Coped With Slippery Slopes
A new investigation of a fossilized tracksite in southern Africa shows how early dinosaurs made on-the-fly adjustments to their movements to cope with slippery and sloping terrain. Differences in how early dinosaurs made these adjustments provide insight into the later evolution of the group.

Quick Rebound From Marine Mass Extinction Event
In 1980, Luis Alvarez and his collaborators stunned the world with their discovery that an asteroid impact 65 million years ago probably killed off the dinosaurs and much of the the world's living organisms. But ever since, there has been an ongoing debate about how long it took for life to return to the devastated planet and for ecosystems to bounce back.

Was Mighty T. Rex 'Sue' Felled By A Lowly Parasite?
In 1980, Luis Alvarez and his collaborators stunned the world with their discovery that an asteroid impact 65 million years ago probably killed off the dinosaurs and much of the the world's living organisms. But ever since, there has been an ongoing debate about how long it took for life to return to the devastated planet and for ecosystems to bounce back.

Dinosaurs had 'earliest feathers'
Exceptionally well preserved dinosaur fossils uncovered in north-eastern China display the earliest known feathers.

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Richard Lenski started an experiment more that 20 years ago in February 1988, every day since then he and his students have carried out the following procedures. By early 2008 45,000 generations of E. coli had been produced under rigorous laboratory conditions.



There are 12 populations of E.coli and all are treated in exactly the same way.

Overview of the E. coli long-term evolution experiment

The inexorable rhythm of the project is as follows:

1. Every day, the cultures are propagated;
2. Every 75 days (500 generations), mixed-population samples are frozen away; and
3. Mean fitness, relative to the ancestor, is estimated using the mixed-population samples.

Note that "3" can be done anytime after "2". Each of these tasks is described in detail below.

For all aspects of this project, unless otherwise stated, the following standards are maintained:

1. The liquid culture medium is DM supplemented with 25 mg/l of glucose;
2. Cells are spread on TA plates; and
3. Liquid cultures and agar plates are incubated at 37C.

Two types of back-ups for the long-term populations are available in the event of a mishap:

4. After each daily transfer, cultures are saved in the refrigerator for one day; and
5. The mixed-population samples are stored indefinitely and can be used to re-start the cultures.

1. Daily transfers

* Daily transfers should be made 22-26 hours after the previous day's transfer.
* Label 12 flasks as A+1 through A+5 and A-1 through A-6. (Check flasks and beaker tops for cracks.) Add 9.9 ml of DM25 to each flask.
* Remove 12 flasks from shaking incubator. Visually confirm (slight) turbidity of each.
* Propagate 12 cultures by transferring 0.1 ml from previous day's cultures into fresh DM25. While transferring, strictly alternate between + and - cultures. This maximizes our ability to detect any inadvertent cross-contamination.
* Incubate the new flasks in the shaking incubator at 37C and 120 rpm.
* Save the old flasks for one day in the refrigerator, discarding the previous day's flasks. (In the event that a flask has cracked, or some other mishap, use the previous day's flasks from the refrigerator, setting the transfer number back by one day.)
* Be sure to record each day in the notebook by day number.

2. Storing mixed-population samples

* Every 75th day ( = 500 generations), the evolving populations are themselves stored away in the ultra-low freezer at -80C.
* Perform the daily transfer as always. Also, plate for colonies to check for contamination.
* Number and label 12 large and 12 small freezer vials. Numbering should begin after the last number used for the entire freezer collection. The large and small freezer vials receive duplicate numbering; the small vials provide back-ups. In addition to putting number stickers on top, use a blue marker to write numbers and strain identifiers on the vials. Record the strain numbers and identifications in the lab notebook, noting in particular that these are "mixed-population samples" (not clonal isolates).
* To each of the previous day's cultures, add glycerol (about 1 ml) from the small tubes. Swirl to mix the glycerol well with the culture; this takes some effort owing to the viscous nature of the glycerol.
* Using an individually wrapped, sterile bulb-pipette for each culture, transfer 1 ml to the appropriate small vial and 5 ml to the corresponding large vial. The vials are then stored away in the appropriate freezer boxes.

The environment was controlled for temperature and availability of nutrients. Without mutation there would have been no change in any of the characteristics of the organism in any of the 12 populations. Just one example of change is shown here Cell Size Data Through Generation 10,000. All the populations started out with an average volume of 0.3725 fL (Femto Litres, 10^-15 L) by the 10,000th generation the average volumes of the cells in all populations had increased within the range 0.655 fL to 1.1 fL. This is just one example of adaption where a larger cell has a reproductive advantage over a smaller cell.

If you wish to read further then I would suggest this .pdf Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli.

The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit⁺) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that ‘‘replayed’’ evolution from different points in that population’s history. We observed no Cit⁺ mutants among 8.4 X 1012 ancestral cells, nor among 9 X 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit⁺, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit⁺ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

If you found that all rather dry a much more accessible description appears in chapter 5 'Before our very eyes' pages 116-133 'Forty-Five thousand generations of evolution in the lab.' if Professor Dawkin's book The Greatest show on Earth.

Article in New Scientist Bacteria make major evolutionary shift in the lab

22:00 09 June 2008 by Bob Holmes



A major evolutionary innovation has unfurled right in front of researchers' eyes. It's the first time evolution has been caught in the act of making such a rare and complex new trait.

And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.

Twenty years ago, evolutionary biologist Richard Lenski of Michigan State University in East Lansing, US, took a single Escherichia coli bacterium and used its descendants to found 12 laboratory populations.

The 12 have been growing ever since, gradually accumulating mutations and evolving for more than 44,000 generations, while Lenski watches what happens.

Profound change

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Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations - the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

"It's the most profound change we have seen during the experiment. This was clearly something quite different for them, and it's outside what was normally considered the bounds of E. coli as a species, which makes it especially interesting," says Lenski.

Rare mutation?

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By this time, Lenski calculated, enough bacterial cells had lived and died that all simple mutations must already have occurred several times over.

That meant the "citrate-plus" trait must have been something special - either it was a single mutation of an unusually improbable sort, a rare chromosome inversion, say, or else gaining the ability to use citrate required the accumulation of several mutations in sequence.

To find out which, Lenski turned to his freezer, where he had saved samples of each population every 500 generations. These allowed him to replay history from any starting point he chose, by reviving the bacteria and letting evolution "replay" again.

Would the same population evolve Cit+ again, he wondered, or would any of the 12 be equally likely to hit the jackpot?

Evidence of evolution

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The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ - and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

In the meantime, the experiment stands as proof that evolution does not always lead to the best possible outcome. Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories.

Lenski's experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. "The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events," he says. "That's just what creationists say can't happen."

Journal reference: Proceedings of the National Academy of Sciences (DOI: 10.1073/pnas.0803151105)

Related article from the New Your Times Fast-Reproducing Microbes Provide a Window on Natural Selection

In the corner of a laboratory at Michigan State University, one of the longest-running experiments in evolution is quietly unfolding. A dozen flasks of sugary broth swirl on a gently rocking table. Each is home to hundreds of millions of Escherichia coli, the common gut microbe. These 12 lines of bacteria have been reproducing since 1989, when the biologist Richard E. Lenski bred them from a single E. coli. “I originally thought it might go a couple thousand generations, but it’s kept going and stayed interesting,” Dr. Lenski said. He is up to 40,000 generations now, and counting.