Two question asked by
@YoursTrue. Answered questions but with no response? What happened?
Items (organisms) are placed there on the various branches, where are the 'proofs' or "evidences" of the in-between organisms? And more specifically, what happened to cause these distinct (other) organisms to come about?
Answering your second question should explain the first as well. I think both questions tie together nicely and are just a simple matter of misunderstanding the process of evolution.
You see natural selection only acts on the population’s heritable traits: selecting for beneficial alleles (an allele is one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome) and thus increasing their frequency (the variant of a gene at a particular point in a population and is the fraction of all chromosomes in the population that carry that alternative gene) in the population, while selecting against deleterious alleles and thereby decreasing their frequency—a process that is adaptive. Natural selection does not act on individual alleles, but on entire organisms. An individual may carry a very beneficial genotype (the genetic constitution of an individual organism) with a resulting phenotype (the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment) that, for example, increases the ability to reproduce, but if that same individual also carries an allele that results in a fatal childhood disease, that fertility or reproductive phenotype will not be passed on to the next generation because the individual will not live to reach reproductive age. Natural selection acts at the level of the individual; it selects for individuals with greater contributions to the gene pool of the next generation, known as an organism’s evolutionary fitness. Fitness is often quantifiable and is measured by scientists in the field. However, it is not the absolute fitness of an individual that counts, but rather how it compares to the other organisms in the population. This concept called relative fitness allows researchers to determine which individuals are contributing additional offspring to the next generation, and therefore, how the population might evolve. There are several ways selection can affect population variation: stabilizing selection (a type of natural selection is which the population mean stabilizes on a particular non extreme trait value. This means that most common phenotype in the population is selected for and continues to dominate in future generations), directional selection (a trend in which an extreme phenotype is favored over other phenotypes, causing the allele frequency to change over time in the direction of that phenotype),
diversifying selection (a mode in which extreme values for a trait are favored over intermediate values and can occur when environmental changes favor individuals on either end of the phenotypic spectrum), frequency-dependent selection (a process whereby the fitness of a phenotype or genotype increases as it becomes more common in a population), and sexual selection (natural selection arising through preference by one sex for certain characteristics in individuals of the other sex). As natural selection influences the allele frequencies in a population, individuals can either become more or less genetically similar and the phenotypes displayed can become more similar or more disparate. So in short there are several different factors that effect genetics and as a result over time these mutations can make a group more or less genetically similar. So for instance genetic mutations occur and the now less genetically similar creatures may change slowly over time, slowly becoming less similar, and passing down genetic mutations and accruing new genetic mutations by either the mutation becoming more prevalent in the group or by environmental changes or sexual preference etc…until they are a new creature. We have found and do find transitional fossils all the time and we use evolutionary taxonomy to arrange and classify them using a combination of progenitor-descendant relationships (serial descent), degrees of evolutionary change, and their phylogenetic relationship (shared descent). You seem like a smart guy. Let me know if you need further clarification.