open access

Today, Svante Pääbo's group at the Max Planck Institute for Evolutionary Anthropology released high-coverage sequence data from a toe bone from Denisova Cave. The new genome comes a year after the same group released the high-coverage genome of the Denisova finger bone, several months before they published the first high-coverage analysis of this ancient genome [1]. Today's announcement is here: "A high-quality Neandertal genome sequence". It adds a second high-coverage genome from Denisova Cave, this one from a toe bone. Unlike the first finger bone genome, this toe has produced a genome very much like Neandertal specimens from much further west, including the Vindija Neandertals.

Something interesting in these data: the presence of a Y chromosome.

There's not so terribly much we can say about a toe. This particular bone was first reported in 2011 by Mednikova [2], who described the specimen's anatomy. She found the toe similar in some respects to equivalent Neandertal toe bones, but also like recent humans in a couple of details. Still, the anatomy wouldn't be enough to conclude that the bone is a Neandertal, because we don't know much about the toes of other ancient human populations.

The genetics are fairly clear about the level of similarity of this new genome to other Neandertals. From the announcement:

The figure shows a tree relating this genome to the genomes of Neandertals from Croatia, from Germany and from the Caucasus as well as the Denisovan genome recovered from a finger bone excavated at Denisova Cave. It shows that this individual is closely related to these other Neandertals. Thus, both Neandertals and Denisovans have inhabited this cave in southern Siberia, presumably at different times.

This is a cluster diagram based on genome-wide similarity, which doesn't tell us about possible mixture among the populations. But it does show the high degree of similarity among the known Neandertals. This new specimen from Denisova (labeled "Altai") is a bit further from them than they are to each other, but not much. It will be interesting to assess this degree of similarity in comparison with the within-population similarity of more living human populations.

I'm reluctant to accept a dichotomy of "Denisovan" versus "Neandertal". Distinguishing the samples in that way invites a typological assumption about the ancient people, giving an impression of distinctness that I'm not yet convinced about. It remains to seriously investigate the hypothesis that one or both of these putative samples represents some amount of gene flow from each other, or from yet more ancient populations. But I suppose we're stuck with the "Neandertal from Denisova" and the "Denisovan from Denisova".

Unless we go for "manual genome" versus "pedal genome", which is admittedly unappealing.

There's not much meat in this announcement, that will wait for the full published analysis that we can expect later this year. The most important aspect of this, like the Denisova data availability from last year, is that we can now start working with the high-quality data. As someone who works with sequences, I cannot overstate the importance of having the best high-coverage data available for our work.

I have a paper in preparation where I make a relevant analogy, in this case noting last year's high-coverage Denisovan genome in comparison to the history of ancient DNA sequencing:

To put this into context: the original 360bp sequence from Feldhofer 1 has been memorialized on a cross-shaped plaque at the site outside Mettmann, Germany. This plaque is approximately 1 square meter in size. A similar monument to contain the Denisova high-coverage data would need to be more than 14 kilometers across. Compared to the first sequencing effort in 1997, today’s state of the art involves the generation of more than 200 million times more data.

It's a pretty awesome time for those of us exploring human evolution!

References

The White House this week announced a new policy on public access to results from federally funded research. The announcement has gotten

Michael Eisen comments: "No celebrations here: why the White House public access policy sucks".

The administration fell hook line and sinker for the ridiculous argument put forth by publishers that the only way for researchers and the public to get the servies they provide is to give them monopoly control over the articles for a year – the year when they are of greatest potential use.

Think about how absurd this is. Publishers, whose role should be to disseminate information as widely as possible, are now the only reason why the public will continue to not have access to research results their tax dollars paid for.

Why is Eisen so exercised? Here's an excerpt from the White House policy memo describing the policy on publication access:

In developing their public access plans, agencies shall seek to put in place policies that enhance innovation and competitiveness by maximizing the potential to create new business opportunities and are otherwise consistent with the principles articulated in section 1.

Agency plans must also describe, to the extent feasible, procedures the agency will take to help prevent the unauthorized mass redistribution of scholarly publications.

In other words, it's no longer just a matter of copyright agreements with publishers; now the federal agencies themselves must help police PDF sharing among researchers. I wonder where "mass redistribution" will kick in.

Further, the memo does not set a 12-month access embargo as a maximum, it directs agencies to adopt the 12-month embargo as a guideline. There is a lot not to like in the memo.

Most of the public attention to the decision has been directed at the effects on scientific publications. I have long been interested in a second area: the public access to data generated by federally funded research.

The White House Office of Science and Technology Policy last year requested public comment on two questions: open dissemination of federally-funded research and open access to data resulting from federally-funded research. I commented last year in response to the OSTP request ("Public interests in data from federally funded research") about the value of data to scientists and others who are not members of federally funded labs. The present announcement from the White House did not indicate how these comments from last year may have contributed to the decision, but it includes general recommendations on both publication and data access.

As it stands, the text of the memo essentially keeps in place the data access requirements established under the Bush administration. That is not a bad thing, and indeed the recommendations listed in the memo seem very reasonable. I quote them here at length:

Each agency’s public access plan shall:

a) Maximize access, by the general public and without charge, to digitally formatted scientific data created with Federal funds, while:

i) protecting confidentiality and personal privacy,

ii) recognizing proprietary interests, business confidential information,and intellectual property rights and avoiding significant negative impact on intellectual property rights, innovation, and U.S. competitiveness, and

iii) preserving the balance between the relative value of long-term preservation and access and the associated cost and administrative burden;

b) Ensure that all extramural researchers receiving Federal grants and contracts for scientific research and intramural researchers develop data management plans, as appropriate, describing how they will provide for long-term preservation of, and access to, scientific data in digital formats resulting from federally funded research, or explaining why long-term preservation and access cannot be justified;

c) Allow the inclusion of appropriate costs for data management and access in proposals for Federal funding for scientific research;

d) Ensure appropriate evaluation of the merits of submitted data management plans;

e) Include mechanisms to ensure that intramural and extramural researchers comply with data management plans and policies;

f) Promote the deposit of data in publicly accessible databases, where appropriate and available;

g) Encourage cooperation with the private sector to improve data access and compatibility, including through the formation of public-private partnerships with foundations and other research funding organizations;

h) Develop approaches for identifying and providing appropriate attribution to scientific data sets that are made available under the plan;

i) In coordination with other agencies and the private sector, support training, education, and workforce development related to scientific data management, analysis, storage, preservation, and stewardship; and

j) Provide for the assessment of long-term needs for the preservation of scientific data in fields that the agency supports and outline options for developing and sustaining repositories for scientific data in digital formats, taking into account the efforts of public and private sector entities.

These recommendations are all basically already in the NSF data access policies, meaning that the new White House memo will maintain the status quo at that level.

The problem is that the current policy is toothless. Continued data access is a very serious problem threatening the integrity of science. Self-archiving and institutional archiving have been sufficient to pass data management portions of grant applications, but have proven to be woefully insufficient to enable access to data. Meanwhile, some fields have intensive data collection but very little or no data entering the public domain as part of digital repositories. The recommendations listed above do nothing to change the current situation.

Nevertheless there is some room within the recommendations for agency directors to take bolder action on data access. Section (j) perhaps provides the best hope. If federal funding agencies actually assess the long-term needs of each field supported by funding, many (including anthropology) will clearly benefit from the establishment of standard digital repositories.

I hope that NSF will not sit on its current policy but will instead work to extend access more broadly. At the same time, I wish the White House had given clearer guidance to enable the creation of digital repositories and to require their standard use as a condition of continued funding of research projects.