A tiny bit of knowledge is a dangerous thing

March 11th, 2012 by PZ Myers

Good news! The gorilla genome sequence was published in Nature last week, and adds to our body of knowledge about primate evolution. Here’s the abstract:

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human–chimpanzee and human–chimpanzee–gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

I’ve highlighted one phrase in that abstract because, surprise surprise, creationists read the paper and that was the only thing they saw, and in either dumb incomprehension or malicious distortion, took an article titled “Insights into hominid evolution from the gorilla genome sequence” and twisted it into a bumbling mess of lies titled “Gorilla Genome Is Bad News for Evolution”. They treat a phenomenon called Incomplete Lineage Sorting (ILS) as an obstacle to evolution rather than an expected outcome.

This problem is related to a biological paradigm called independent lineage sorting. To illustrate this concept among humans and primates, some segments of human DNA seem more related to gorilla DNA than chimpanzee DNA, and vice versa. This well-established fact produces different evolutionary trees for humans with various primates, depending on the DNA sequence being analyzed.

In a significant number of cases, evolutionary trees based on DNA sequences show that humans are more closely related to gorillas or orangutans than chimpanzees—again, all depending on which DNA fragment is used for the analysis. The overall outcome is that no clear path of common ancestry between humans and various primates exists, so no coherent model of primate evolution can be achieved.

The recent release of the gorilla genome spectacularly highlights this evolutionary quandary. According to the Nature study, “in 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other.”

When you compare the genomic sequences of three related species, such as the human, chimp, and gorilla, you’ll typically find from an average that a pattern of relatedness is revealed: humans and chimps are closer to each other than they are to gorillas, indicating a more recent divergence between humans and chimps than between humans and gorillas. However, that’s an average result: if you compare them base by base, you’ll find genes and regions of the chromosomes in which the gorilla sequence is more similar to the human sequence than to the chimpanzee sequence; if you looked at only that gene, you’d conclude that humans and gorillas were closer cousins, and chimpanzees were more distant.

Is ILS a problem? It complicates the analysis of sequences for sure (although it also can be used as a probe to look at evolution). But it’s not a problem that calls evolution into question; to the contrary, it’s an expected phenomenon.

Here’s why. This diagram illustrates the simplistic, naïve expectation you might have.