Demonstrable and repeatable examples of evolution

Question

Are there examples of evolution that can be demonstrated as proof that evolution occurs and is a useful mechanism for making predictions?

Some examples that come to mind include:

1. Animal husbandry (e.g. cattle, dogs, etc.);
2. Bacteria that survive antibiotics evolving resistance;
3. Statistics on human eye color.

I'd like to know what other examples are out there, and which would be the most apparent or persuasive for convincing those skeptical of the evolutionary process.

Answer 1

The question is way too wide to be answered here in full, however I gathered some evidence for you to get you started.

Websites

Evowiki.org seems to incorporate a significant portion of the content of TalkOrigins.org (below), and continues to be updated. Evowiki is also presented in the more contemporary MediaWiki format.

TalkOrigins.org is an archive of evidence behind evolution, arising out of discussion on the Usenet group talk.origins since 1986. They present no less that 29 pieces of evidence of it (confirmed by multiple studies, in principle disprovable by experiment). Note: TalkOrigins.org doesn't seem to have been updated since 2006.

Summary of evidence

As presented by TalkOrigins.

A unique, historical phylogenetic tree

1. Unity of life
   All species that we know of share the same basic biochemical building blocks of life, like polymers, metabolism, etc.
2. Nested hierarchies
   We have a tree of species, not a simple list
3. Convergence of independent phylogenies
   The tree of life is supported both by the morphology of the species (the phylogenetic tree, how it was originally conceived) and the molecular similarities of the DNA.
   • Statistics of incongruent phylogenies
     Not only the phylogenetic tree and the molecular tree are correlated, but the correlation has a p-value ≤ 7.4 × 10^–8.
4. Transitional forms
   All fossilized animals found conform to the standard phylogenetic tree.
   • Reptile-birds
   • Reptile-mammals
   • Ape-humans
   • Legged whales
   • Legged seacows
5. Chronology of common ancestors
   Fossilized intermediates appear in the correct general chronological order based on the standard tree.

Past history

1. Anatomical vestiges
   The various nonfunctional or rudimentary vestigial characters, both anatomical and molecular, that are found throughout biology.
2. Atavisms
   An atavism is the reappearance of a lost character specific to a remote evolutionary ancestor and not observed in the parents or recent ancestors of the organism displaying the atavistic character.
   • Whales and dolphins with hindlimbs
   • Humans tails
3. Molecular vestiges
   Vestigial characters are also found at the molecular level.
4. Ontogeny and developmental biology
   The morphological aspect of embryos.
   • Mammalian ear bones, reptilian jaws
   • Pharyngeal pouches, branchial arches
   • Snake embryos with legs
   • Embryonic human tail
   • Marsupial eggshell and caruncle
5. Present biogeography
   Because species divergence happens not only in the time dimension, but also in spatial dimensions, common ancestors originate in a particular geographical location. In fact, the spatial and geographical distribution of species is consistent with their predicted genealogical relationships.
6. Past biogeography
   Past biogeography, as recorded by the fossils that are found also conforms to the standard phylogenetic tree.
   • Marsupials
   • Horses
   • Apes and humans

Evolutionary opportunism

1. Anatomical parahomology
   Parahomology, as the term is used here, is similarity of structure despite difference in function. When one species branches into two species, one or both of the species may acquire new functions. Since the new species must recruit and modify preexisting structures to perform these new functions, the same structure shared by these two species will now perform a different function in each of the two species.
2. Molecular parahomology
   The concept of parahomology applies equally to both the macroscopic structures of organisms and structures on the molecular level.
3. Anatomical convergence
   Analogy is the case where different structures perform the same or similar functions in different species. Two distinct species have different histories and different structures; if both species evolve the same new function, they may recruit different structures to perform this new function.
4. Molecular convergence
   Like parahomology, analogy should be represented on both macroscopic and molecular levels.
5. Anatomical suboptimal function
   Evolutionary opportunism also results in suboptimal functions and structures.
6. Molecular suboptimal function
   The principle of imperfect design should apply to biomolecular organization as well.

Molecular evidence

1. Protein functional redundancy
   The support for common descent given by studies of molecular sequences can be phrased as a deductive argument
2. DNA functional redundancy
   Like protein sequence similarity, the DNA sequence similarity of two ubiquitous genes also implies common ancestry.
3. Transposons
   In many ways, transposons are very similar to viruses. However, they lack genes for viral coat proteins, cannot cross cellular boundaries, and thus they replicate only in the genome of their host. They can be thought of as intragenomic parasites.
4. Redundant pseudogenes
   Pseudogenes have faulty regulatory sequences that prevent the gene from being transcribed into mRNA, or they have internal stop codons that keep the functional protein from being made.
5. Endogenous retroviruses
   Endogenous retroviruses are molecular remnants of a past parasitic viral infection.

Change

1. Genetic
   Genotype specifies possible phenotypes, therefore, phenotypic change follows genetic change.
2. Morphological
   Macroevolution requires that organisms' morphologies have changed throughout evolutionary history; in fact, we do observe morphological change and variation in modern populations.
3. Functional
   The ability to occupy one niche over another is invariably due to differing functions. Thus, functional change must be extremely important for macroscopic macroevolutionary change.
4. The strange past
   More recent fossils are more similar to contemporary life forms than older fossils.
5. Stages of speciation
   We see all possible degrees of speciation or genetic isolation today, ranging from fully interbreeding populations, to partially interbreeding populations, to populations that interbreed with reduced fertility or with complete infertility, to completely genetically isolated populations.
6. Speciation events
   The standard phylogenetic tree illustrates countless speciation events; each common ancestor also represents at least one speciation event. Thus we should be able to observe actual speciation, if even only very rarely.
7. Morphological rates
   Observed rates of evolutionary change in modern populations are greater than or equal to rates observed in the fossil record.
8. Genetic rates
   Rates of genetic change, as measured by nucleotide substitutions, must also be consistent with the rate required from the time allowed in the fossil record and the sequence differences observed between species.

Books

There's plenty of evidence in these books

• Charles Darwin, "On the origin of the species".

The book is mostly concerned with experimental evidence

• Richard Dawkins, "The greatest show on Earth"

The entire book is about this.

Answer 2

I would say that the most important and, in my opinion as a bioinformatician, the most interesting, evidence for evolution is found in the thousands of whole-genome DNA sequences from a wide array of species obtained in the past 33 years.

If the sequences are compared to each other, cladistic analysis and the principle of maximum parsimony can be used to map out a tree of these sequences. This tree, in virtually every case, matches perfectly with the phylogenic tree of life obtained from the fossil record through comparative homology. I would provide some references for this claim but I'm limited to 2 links, but Google Scholar is an excellent resource.

Darwin had no idea that genes or DNA existed when he wrote "On the Origin of Species", but over 100 years later there is yet another large body of direct, objective evidence for the common descent of life on Earth. People who deny evolution just do not understand that when there is this amount of evidence for a theory, it would take an equal or greater amount of evidence to disprove it, and an explanation as to why the current body of evidence looks correct but isn't. In any real science, there are always controversies and unsolved problems. We have no idea what exactly it is that causes gravity, but no reasonable person doubts that gravity exists.

Answer 3

From stackexchange.biology Evolution in 37 Years, is it possible? is quite an example for this question. It investigates the speciation of two lizard groups in 37 years:

In 1971, biologists moved five adult pairs of Italian wall lizards from their home island of Pod Kopiste, in the South Adriatic Sea, to the neighboring island of Pod Mrcaru. Now, an international team of researchers has shown that introducing these small, green-backed lizards, Podarcis sicula, to a new environment caused them to undergo rapid and large-scale evolutionary changes."