john hawks weblog

paleoanthropology, genetics and evolution

broadly consistent watch

  • Finding where datasets line up

    Wed, 2011-12-07 18:44 -- John Hawks

    Adam Van Arsdale comments on a new paper [1] that tries to correlate variability in paleoclimates with human evolutionary events: "Paleoanthropology with 3D glasses".

    Separate from their analysis of the climate data, the authors conclusion regarding human evolution is based on the correlation between their climate analyses and a specific human evolutionary model. Given a different model (part E of the figure above), this correlation wouldn’t necessarily exist. And yet this kind of approach, combining information from different (hopefully somewhat independent) lines of evidence to address single hypotheses, is what paleoanthropology is primed for.

    He hat tips the "Broadly Consistent Watch" feature here, which I badly need to revive...


    References

    1. Donges JF, Donner RV, Trauth MH, Marwan N, Schellnhuber H-J, and Kurths J. 2011. Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution. Proceedings of the National Academy of Sciences of the United States of America.
  • BROADLY CONSISTENT WATCH II

    Sun, 2005-10-02 23:14 -- John Hawks

    Looking back through the Chimpanzee Genome Consortium (2005) paper, I find this:

    Chimpanzee polymorphisms. The draft sequence of the chimpanzee genome also facilitates genome-wide studies of genetic diversity among chimpanzees, extending recent work. We sequenced and analysed sequence reads from the primary donor, four other West African and three central African chimpanzees (Pan troglodytes troglodytes) to discover polymorphic positions within and between these individuals.

    A total of 1.66 million high-quality single-nucleotide polymorphisms (SNPs) were identified, of which 1.01 million are heterozygous within the primary donor, Clint. Heterozygosity rates were estimated to be 9.5 x 10-4 for Clint, 8.0 x 10-4 among West African chimpanzees and 17.6 x 10-4 among central African chimpanzees, with the variation between West and central African chimpanzees being 19.0 x 10-4. The diversity in West African chimpanzees is similar to that seen for human populations, whearas the level for central African chimpanzees is roughly twice as high.

    The observed heterozygosity in Clint is broadly consistent with West African origin, although there are a small number of regions of distinctly higher heterozygosity. These may reflect a small amount of central African ancestry, but more likely reflect undetected regions of segmental duplications present only in chimpanzees (Chimpanzee Genome Consortium 2005:70, emphasis added).

    I included the context before the "broadly consistent" to be clear about what it refers to. Elsewhere in the article, the consortium identifies "Clint" as a "captive-born descendant of chimpanzees from the West Africa [sic] subspecies Pan troglodytes verus" (CGS 2005:70). So Clint's heterozygosity isn't just broadly consistent with West African origin; it is an example of West African origin.

    Now, the "broadly consistent" is there because the overall heterozygosity estimate for Clint is a bit higher than typical for West African chimps. So why don't they just say that? It's not like Clint's origin is a mystery.

    And there are plenty of good hypotheses for why one captive-born chimpanzee might have slightly higher overall heterozygosity than other members of his subspecies. The paper lists two; others include the possibility that Clint's captive ancestors were taken from different parts of West Africa, or that the captive breeding program avoided inbreeding more than wild chimpanzees. Any of these might be tested; they weren't, so we're left with the "broadly consistent" answer.

    Synopsis: 
    Here, "broadly consistent" means, we didn't bother to test the specifics.
  • BROADLY CONSISTENT WATCH I

    Fri, 2005-09-23 00:12 -- John Hawks

    I'm starting a new tradition here, the "Broadly Consistent Watch." If you see that headline, you can be sure I'll be noting an abuse of the term "broadly consistent" --- indeed, in most cases, I'll be pointing out the use of the term for things that are actually not consistent at all.

    Here's the first edition, from Kivisild et al. (2005:10) (also discussed in a previous post):

    The coalescent date of the human mitochondrial DNA tree using this rate is 160,000 (S.D. 22,000) years. This coalescent date is broadly consistent with the dates of the Homo sapiens fossils recognized so far from Ethiopia (CLARK et al. 2003; MCDOUGALL et al. 2005; WHITE et al. 2003).

    This is an excellent example of the au courant use of the term. Here, the paper shows its familiarity with the recent literature on fossil hominids, correctly citing the recent Omo Kibish dates and Herto fossils. And indeed the Herto fossils are dated to between 154,000 and 160,000 years ago, and the Omo Kibish hominids between 190,000 and 200,000 years, so these "early modern" humans do appear to be "broadly consistent" with the mtDNA coalescence estimate.

    But that's the beauty of "broadly consistent": it can apply to anything within a ballpark or two (or four), especially if (a) you're talking about data from another field, and (b) you don't look too closely at the numbers.

    It's so tempting just to say "broadly consistent" and let the minds of the readers connect the dots: "Aha! It proves the theory! This can't be a mere coincidence! The dates are broadly consistent!" It's so tempting almost no one can resist using it from time to time.

    Let's look more closely at these "broadly consistent" dates. First of all, the Omo Kibish hominids simply fall outside the standard error of the mtDNA date. They're not "broadly consistent" at all --- if anything, they appear to be inconsistent, although they probably are close enough to be within a 95 percent confidence interval (if it were reported, which it isn't).

    That assumes that the important thing is for the dates to be the same. But if the human mtDNA type supposedly came from the population represented by these Ethiopian Homo sapiens fossils, then its variation must coalesce before these fossils. The same date is not evidence for consistency; a consistent date would be earlier. How much earlier depends on the demography, but 10 or 20 thousand years would seem like a bare minimum.

    And then there's the "hotspot" problem that is the subject of the Kivisild et al (2005) paper. The 160,000 year estimate assumes equality of rates among sites, but the data indicate that some sites mutate much more frequently than others, and repeatedly during human evolution. If these sites mutate more rapidly and have saturated on the human lineage compared to chimpanzees, then the 160,000 year date should be an overestimate because humans should have more variation than expected from the long-term evolutionary comparisons. The data do not indicate how extensive this overestimate may be, but it makes the coalescence less consistent with the dates of the fossils, not more.

    Now, can we say in this case that the dates are really not "broadly consistent"? No, indeed we can't. There are just too many sources of error in the genetic estimate to say whether it might be within the range of possible mtDNA ancestors of these Ethiopian fossils. The date could be as high as 210,000 - 220,000 years, if the mutation rate has been overestimated (e.g., if many rare sites that currently segregate are in fact selected). From that perspective, the dates are "broadly consistent" with every event in the Late Pleistocene.

    But that's far from a vote of confidence. It is not a significant coincidence; it is the overlap of uncertainty. And that's usually what "broadly consistent" means.

    References:

    Kivisild T et al. 2005. The role of selection in the evolution of human mitochondrial genomes. Genetics (online before print).

    Synopsis: 
    I introduce a new feature, looking for cases where two huge confidence intervals slightly overlap.
Subscribe to broadly consistent watch

Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.