Due to the fact that religion and evolution are such hot topics in the off topic forum, I've decided to compile this list as a reference. It will make it much easier than having to type the same things over and over again. As my profile says, I am majoring in evolutionary biology. However, none of this is my own research. I'm no where near far enough along into my studies to begin coming up with new ideas. These are all taken from my biology text book.

Keep in mind, Darwin did not prove evolution. Even in Darwin's time, evolution was fairly well accepted. What wasn't known however was the mechanism that caused evolution. This is what Darwin contributed to science. His contribution to science was his proposal that evolution occurred through natural selection.

Darwin's Finches
One of the locations that Darwin visited during his almost five year voyage aboard the HMS Beagle were the Galãpagos Islands. There he collected 31 specimens of finches from three islands. In all, there were 14 species collected. Darwin noticed that there was a correspondence between the beaks of the finches and their food source. This suggested to him that natural selection had shaped them.

Now, by itself this wouldn't be considered solid evidence. Fortunately, there is more to tell. Natural Selection requires that three conditions must be met: (1) Variation must exist in the population; (2) this variation must lead to differences among individuals in survival and reproductive success; and (3) variation among individuals must be genetically transmitted to the next generation.

Starting in 1973, Peter and Rosemary Grant and generations of their students studied the medium ground finch known as Geospiza fortis. These finches primarily feed on seeds that are produced in plants during wet years. They will eat larger seeds, but only during the dry years because the larger seeds are harder for the finches to crush. The Grants discovered that the average beak depth of the finches changed from one year to the next in a predictable fashion. During dry seasons, the birds with the larger beaks survived, were able to reproduce, and thus the population of larger beaked finches increased. Once the wet years returned, the average beak size decreased since the birds with the smaller beaks were able to survive longer and reproduce.

The Peppered Moth
The peppered moth, Biston betularia, is another example of natural selection at work. The adult moth comes in several shades that range from light grey to jet black. Genetic analysis has revealed that the color of the moth is coded by different alleles of a single gene. The allele that colors the moth black is dominant over the allele that colors the moth grey, however prior to 1850, the black moth was very rare. From 1850 and on, the population near industrialised centers began to increase until it they made up nearly 100% of the population. The soot from the factories had covered the trees that the moths rested on. Being black gave the moths a natural camouflage, thus they were not eaten by the birds the fed upon them. Instead, the birds at the grey moths which clearly stood out on the black colored trees. Again, natural selection at work.

Artifical Selection
Humans have used selection since the dawn of civilization. We artificially select organisms based on the phenotypic traits that we desire. It is used in lab experiments, agriculture, and the domestication process. In almost every case that it has been applied, there has been substantial change. This is strong evidence that selection is an effective evolutionary process.

The Fossil Record
Even though fossilization is extremely rare, enough have been discovered to provide a sufficient picture of evolution through the course of history.

When the fossils are arranged according to their age, from youngest to oldest, they often provide a picture of evolutionary change.

The Evolution of Horses
The evolution of the horse is one of the best studied fossil record cases. The earliest known members of the horse family, didn't look much like the horses of today. They were small, had short legs, and broad feet.

Examination of the fossil record shows how species in the genus Hyracotherium ( which is the earliest known horse family ) has increased in size, has gone from having four toes on its front feet and three on its rear to a single toe, and has gone from small and relatively simple tooth shape to the large complex tooth shape of modern day horses.

All of these changes can be understood as adaptations to changing global climate. During the late Miocene and early Oligocene epochs ( about 20 to 25 million years ago ), grasslands became widespread in North America where most of the evolution of the horse occurred. High speed became important to escape predators, and the teeth changed due to horses eating grass and other vegetation.

The Anatomical Record
As vertebrates evolved, the same bones were sometimes put to different uses. However, the bones are still seen, betraying their evolutionary past. The forelimbs of vertebrates are a good example.


Although the structure of the bones show considerable differences in form and function, the same basic bones are present in all of them. Why should these very different structures be composed of the same bones? If evolution had not occurred, what could explain this?

A comparison can also be made on how organisms develop. For example, early in their development both humans and fish embryos both possess pharyngeal pouches, which in humans develop into various glands and ducts and in fish turn into gill slits. At a later stage, every human embryo has a long bony tail, which the vestiges of we carry to adulthood as the coccyx at the end of our spine. Human fetuses even possess a fine fur during the fifth month of development. These strongly suggest that our development has evolved, with new instructions modifying ancestral developmental patterns.

The Molecular Record
Our evolutionary past can also be seen at the molecular level. Identical twins in humans are produced when a fertilized egg splits. Since the egg has already been given the separate 23 chromosomes from the father's sperm, the DNA of the two eggs are exactly the same. This is why twins look identical to each other.

Carrying this one step further, we can also see why siblings often times share similar features. Since each was produced from the same mother and the same father, they are going to have similar genes, thus they are going to be similar in appearance.

Applied to other organisms, it is reasonable to surmise that as the similarities between organisms decrease, the genetic makeup of the organisms will also begin to differ. Below is a picture that shows the amino acid differences between hemoglobin of vertebrate species and that of humans.


Using this information, as well as the fossil record, we can see that closely related species are found to be more similar. When the DNA itself is compared, similar patterns also become evident. Since DNA is the genetic code that produces the structures of living organisms, it is expected that groups that appear similar, such as chimpanzees and humans, to be more similar than organisms that are more dissimilar, such as frogs and humans. Even if evolution were not true, this expectation would hold. However, it's important to note that DNA is composed of long stretches of non-coding sequences. This is referred to as "junk DNA". As far as we can tell, these stretches of junk DNA have no function and serve no purpose. If evolution had not occurred, there would be no reason to expect similar-appearing species to also be similar in their junk DNA. Comparisons of such stretches of DNA however provide the same results as for other parts of the genome. Closely related species are more similar, an observation that only makes sense if evolution has occurred.

Hopefully as you read this you learned some things that you didn't know before. If you have any questions, feel free to send them to me and I'll do my best to answer them.
 
Resources:

Raven, Johnson, Losos, Singer. 2005. Biology, seventh edition. McGraw-Hill Custom Publishing. p 454-466.