Wednesday, March 11, 2015

Genomic analysis paints the picture for our primate ancestry

Genomic Analysis Paints the Picture for our Primate Ancestry

               Genome sequencing technology is breaking new ground on the human genome by studying our genetic neighbors. The very first non-human primate genome that was sequence and published is the chimpanzee, using shotgun de novo assembly. With the exception of gibbons, every hominid species has its genome fully sequenced. With all this genomic data, we can paint an incredibly accurate phylogenetic tree. Before, we would make trees using only one gene as a reference, which would lead to false positives on which species were more closely related. If we observed just one gene, we could come to different conclusions. For example, one particular gene between gorillas and humans may be coincidentally close, and if we use that gene as a basis, then we would come to the conclusion that humans are most closely related to humans. We're fairly certain that this isn't true, because we've used the entire genome to get an average of closeness for each gene. Our current model looks like the tree below;
Primate phylogenetic tree.
                How do we reach these conclusions with DNA? A lot of techniques revolve around comparing the percent of similar DNA of specific types. Humans and chimpanzees have DNA that has about 1.4% difference in DNA, but this only accounts for nucleotide substitutions, not for small insertions and deletions in the genome. When you compare small insertions and deletions, the differences get much bigger. What's the value to this? The more differences we can discern from DNA, the easier it becomes to differentiate them. We're no longer working with fraction percent differences, and it becomes much clearer who is closely related and who is not. Insertions and deletions may account for major evolutionary mutations, so they cannot be ignored.

                Even if you think DNA is totally bogus, scientists make an effort to support their claims with interdisciplinary evidence. Scientists have retroactively supported their theories on the close relation to bonobos and chimpanzees by observing their behavior and examining the ecological past of their environment. Bonobos have a matriarchal society where females form close bonds to gain an advantage against males. Chimpanzees don’t have this behavior. Scientists believe this has to do with the feeding opportunities that these species have experienced in their evolutionary past. The common ancestor of chimps and bonobos once coexisted with gorillas, which consumed all the food on the ground and forced the ancestor to be arboreal to eat tree food. At some point, this environment suffered a drought, so the ground plants and gorillas were wiped out as a result. The chimp ancestors were able to survive, and once the ground plants grew back (and the gorillas didn’t), the chimps were able to capitalize on the abundance of food. These chimps eventually evolved into bonobos.
There is a video on national geographic that details it here.

Posted by Patrick O'Loughlin


  1. I am happy to know that there is progress in sequencing these species so a more clear phylogenetic tree can be made. I always found evolution to be interesting, and liked to see how closely related different species are.
    I just wanted to point out to you that I think there are a few typos in your post. In this sentence: "For example, one particular gene between gorillas and humans may be coincidentally close, and if we use that gene as a basis, then we would come to the conclusion that humans are most closely related to humans, even though we’re fairly certain this isn’t true." I think you meant to say gorillas instead of humans twice. So you should probably re-read your post again to make sure you didn't miss any other typos.
    Good post though!
    -Ashley Condon

  2. I went ahead and fixed the typos you highlighted. It may come as no surprise that I was in a state of fatigue while writing my post and I was impressed with just how many mistakes I missed the first time around.
    It is indeed interesting just how closely related these species are, but that closeness is also what makes phylogeny so difficult. We can't rely on morphological differences to do all the work; with species this similar such differences can be misleading. For example, one could come to the conclusion that chimps are more closely related to gorillas than humans, based on morphology. Observing genetic information, we know this isn't true. This is why it's so important to observe as much genetic information as possible, including the small indels that once seemed too numerous to compare.
    -Original poster, Patrick O'Loughlin