Monday, October 1, 2012

Carnival of Evolution, Number 52 — the Network Edition

Welcome to the 52nd edition of the Carnival of Evolution, hosted here at The Genealogical World of Phylogenetic Networks blog.


For those of you not familiar with the Carnival of Evolution, at the beginning of every month the Carnival provides a collection of some of the most interesting of the recent blog posts about biological evolution. The Carnival is hosted by a different blog every month: last month's Carnival can be found at The Stochastic Scientist blog; and next month's Carnival will be hosted by the Sorting Out Science blog at the beginning of November.

The theme for the presentations this month is, of course, phylogenetic networks. You can skip straight on to the blog posts if you are familiar with such networks.

Introduction to phylogenetic networks

For those of you not familiar with phylogenetic networks, the host blog this month is about the use of networks in evolutionary analysis, as a replacement for (or an adjunct to) the usual use of phylogenetic trees. The 46th edition of the Carnival of Evolution (hosted at the Synthetic Daisies blog) provided a good introduction to trees in the study of evolution, which are used as a metaphor for branching genealogical history. In this blog, we take evolutionary trees to the next logical stage — reticulating networks.

Networks have received considerable attention in the recent biological literature, not least in microbiology (where horizontal gene transfer is often considered to be rampant) and botany (where hybridization has always been considered to be common). It has also received increasing attention in the computational sciences.

Networks are acknowledged to have two main uses within phylogenetics: (i) exploratory data analysis, in which conflicting data patterns are displayed and their quality and quantity assessed; and (ii) evolutionary analysis, in which the historical (genealogical) patterns involve not only vertical descent (parent to offspring) but also reticulations due to horizontal processes (such as horizontal gene transfer, hybridization, recombination, and genome fusion).

A network is thus more general than a tree (or "more complete"), because it is a tree that also has reticulations. For example, the Decision Tree presented with the Carnival of Evolution #46 might look like this if it was a network:

Note that for some of the leaves there are multiple paths through the network from the root, whereas a tree is restricted to a single path between any two points. This is the essence of why networks are being introduced into evolutionary studies, because the evolutionary history of many organisms involves complex pathways of "descent with modification" (as Darwin put it).

If you would like to know more about this blog, then the simplest access is via the various Pages, listed at the top of the right-hand column, which gather together the blog posts related to particular topics. The most popular blog posts for non-specialists are in the History and the Analyses sections, as well as in the Tattoo section; so please take a look around the blog while you are here.

This month's Carnival posts

For this edition of the Carnival of Evolution, the featured posts have been incorporated into a series of phylogenetic networks. Each network represents a typical topology that you might encounter in the scientific literature, illustrating the relationships between the blog posts. I have been somewhat selective this month, by not including anything about the ongoing arguments between evolutionists and creationists.

Posts about networks

To get the Carnival off on the right foot, we will start with a collection of blog posts that are themselves about biological networks. They are all different, and not all of them involve phylogenetic networks, so they display the diversity of what networks are used for in biology. The network shown here is a NeighborNet, which connects the topics based on overall similarity.

Franklin Harold, guesting at the Small Things Considered blog, discusses the evolution of the eukaryotes in Begetting the Eukarya: an unexpected light. The eukaryotes originated from the fusion of several genomes, so that the Tree of Life is not a tree at that point in evolutionary history. Sadly, in this blog post the suggested alternative image to a tree is not a network but "a pointed Gothic arch thrusting out of the prokaryotic underbrush", which you will have to check out for yourselves.

John Hawks, at his personal blog, introduces us to the world of human evolution when he explores Denisova at high coverage. The archaic Neandertals and Denisovans have recently been shown to have been involved in gene flow with early modern humans, which re-writes the story of human evolutionary history.

The Genealogical World of Phylogenetic Networks then asks, in light of this information, Why do we still use trees for the Neandertal genealogy? Clearly, a network is more appropriate than a tree for phylogenetic analysis when there is horizontal gene flow.

Razib Khan, at the Gene Expression blog, develops this theme in Across the sea of grass: how Northern Europeans got to be ~10% Northeast Asian. He takes us into more modern times when he ponders recent evidence concerning the evolutionary relationships between Neolithic farmer migrants and the indigenous Mesolithic southern European populations.

Dienekes Pontikos, at his Anthropology Blog, then ponders Structural stability and ancient connections between languages, in which a phylogenetic network is used to discover unexpected geographic clusters of similarity among the families of modern languages.

On a related topic, Jeremy Yoder, The Molecular Ecologist, considers! by looking at ways to summarize multivariate geographical patterns among human genotypes. Sadly, this inadvertently demonstrates just why one should not use Principal Components Analysis for this type of data analysis — the right idea but the wrong tool. The second axis of the ordination is frequently nothing more than a quadratic function of the first axis (ie. a mathematical artifact), as shown clearly by two of the three ordinations reproduced in the blog post. This is one of several reasons why we should use a network instead of PCA.

Bradly Alicea, writing at the Synthetic Daisies blog, then moves away from phylogenetic networks and into gene regulatory networks, with Cascades in common: biological network function in evolution. He connects these networks to biological evolution by pointing out that they contribute to both adaptive variation and to variation between species.

Finally, the ever-present Bjørn Østman, from the Pleiotropy blog, considers Epistasis in evolution. He uses genetic interaction networks to look at epistatic interactions (which are non-additive interaction effects resulting from mutations) and their role in evolution, particularly in adaptation and speciation.

Human evolution

Human evolution is always of interest to humans, and so there is a steady stream of blog posts about this topic every month. The network shown here is a Recombination network, with the converging pair of arrows indicating, in this case, a topic that combines two of the others.

This month, Kathy Orlinsky, writing as The Stochastic Scientist, discusses recent evidence that Our methylomes make us human. One explanation for how humans and chimpanzees can be so different when their genomes are so similar is that the DNA methylation of their genes is different.

On a slightly more tasty note, Heather Pringle, from The Last Word On Nothing blog, considers The sweetness of human evolution. The search for a honey diet has probably played a much more complex (and interesting) role in human history than you have heretofore realized.

Writing at the Nothing in Biology Makes Sense! blog, Jonathan Yoder then muses, appropriately enough, about the Evolution of diabetes? Type 2 Diabetes is a highly multifactorial disorder, so don't expect an answer any time soon.

Gunnar De Winter, masquerading as The Beast, The Bard and The Bot, then contemplates fatty brains and what their genes might tell us about history, in Once upon a (complicated) time in Africa.

Next, Faye Flam, from the Planet of the Apes, ponders What whales tell us about the evolution of menopause. Very few species have a long post-reproductive period for females, and these include several species of whale as well as humans, so a comparative analysis might be very revealing.

Ed Yong, over at the Not Exactly Rocket Science blog, continues the cetacean theme with Same gene linked to bigger brains of dolphins and primates — in this case, the title says it all.

Finally, Helen Thompson and Shankar Vedantam, writing at The Salt blog, reflect on How food and clothing size labels affect what we eat and what we wear. This is my personal favorite post of the month, because it tells us everything we need to know about human evolution.

The study of heterozygosis

Bodies are interesting things, especially the differences between males and females, and this month we have a few blog posts about that topic. The network shown here is a Hybridization Network, in which the paired arrows indicate three hybridization events, in this case showing hybridization of topics based on sex (male versus female).

PZ Myers, over at the Pharyngula blog, shows a great interest in reconstructing reproductive anatomy, in O brave new world that has such penises in't. I'm sure that you will be just as interested in regrowing penises as he is.

Emily Weigel, on the other hand, shows that the Beacon blog is more interested in Maternal effects — mothers have more of an effect on their offspring than most daughters ever want to admit.

As a compromise position, Jerry Coyne, at the Why Evolution is True blog, contemplates A gynandromorph cardinal. Externally, one half of the bird is male and the other half is female, divided lengthwise! A similar thing happens in fruitflies, although they take it to the extreme.

Marc Srour, over at the Teaching Biology blog, then muses about Wolbachia: the ubiquitous male-killing, feminising parasite, which has at least four different ways to alter the insect host's reproduction in order to increase its own maternal transfer.

Finally, Suzanne Elvidge, at the Genome Engineering blog, reports about Men on your mind: male DNA in women’s brains — this concerns the first description of male microchimerism in the female human brain.

Evolutionary theory

Theory is either fascinating or terribly dull, depending on whether you like to spend your time in the pub or in the field. There is room in the world for both types of scientist, and this collection of posts comes from the former group. The network shown here indicates that there is no particularly close relationships among the blog posts.

Joachim Dagg, living in the Mousetrap, starts us off by conducting a Thought experiment about recombination. The resulting conclusion is that the maintenance of sex is a problem distinct and separate from the maintenance of recombination rates.

Jeremy Yoder, still at The Molecular Ecologist blog, reflects on the problem of Isolating isolation by distance — in population genetics, can we distinguish isolation by distance from population structure? The answer appears to be rather complicated.

Ford Denison, at the This Week in Evolution blog, provides us with some thoughts that the editor excised from his book on Darwinian Agriculture, when he asks Biomimicry of forests or trees? The answer is presented as a Galilean dialog between an engineer and a couple of expert biologists.

Andrew Hendry, contributing to the Eco-Evolutionary Dynamics blog, ponders the difficulty of making arguments for biodiversity preservation solely from a consideration of ecosystem services, in Ecosystem disservices and assisted elimination.

Finally, The Genealogical World of Phylogenetic Networks reflects on Metaphors for evolutionary relationships, which surveys the rich world of evocative metaphors used in evolutionary studies.

Evolution in practice

This collection of posts comes from those scientists who have been contemplating the evolving world from inside the lab or out in the field. The network shown here is a Median Network, which simply displays all of the character-state differences between the posts (the central structure is a cube in this case).

The Mostly Open Ocean blog muses about Rapid speciation in starfish. There have been profound changes to life history in the two daughter species arising from the recent speciation event, involving selection on many morphological and physiological traits.

Carl Zimmer, weaving at The Loom blog, revisits one of his favorite experiments in The birth of the new, the rewiring of the old. The experiment is Richard Lenski's 24-year study of evolutionary change in Escherichia coli, which now encompasses an unheard-of 55,000 "generations". The results to date are, to say the least, fascinating.

Ken Weiss, contributing to The Mermaid's Tale, discusses the opposite trend in stay the same? — the horseshoe crab seems to have changed very little for 150 million years.

Jerry Coyne, still at the Why Evolution is True blog, reflects on the same phenomenon in Horseshoe crabs aren’t really "living fossils", but he elaborates instead on some of the differences between the fossil and contemporary species.

Finally, Greg Laden, popping up at the 10,000 Birds blog, contemplates The incredulous New Caledonian crows, which apparently can distinguish the concept of an Unknown Causal Agent from that of a Hidden Causal Agent, which most animal species cannot do.

The ENCODE debacle

The network shown here is a Horizontal Transfer Network, with the two dashed lines showing the transfer of text (quotations) in this case.

Early in the month we saw what may well be the nadir of scientific journalism, when the ENCODE (Encyclopedia of DNA Elements) consortium provided the excuse for a media blitz associated with the co-ordinated release of 30 papers in some of the high-profile genome-oriented journals. Most notably, the media reports focussed almost entirely on the apparently new claim that 80% of human DNA is not "junk" (as opposed to the previous claim that 80% is junk DNA). This new claim rests almost entirely on a re-definition of "junk DNA" rather than any new data about DNA function, so this is not much of a contribution from the ~400 ENCODE people, let alone a good reason for a media bombardment. Not unexpectedly, the blogsphere exploded with outrage at the distortions involved in the media reporting. A few selected blog posts are included here to commemorate the event.

Mike White, sitting in The Finch and Pea pub, sets the scene with ENCODE media fail (or, Where’s the null hypothesis?). Michael Eisen, at the It Is NOT Junk blog, then starts the attack on the media with This 100,000 word post on the ENCODE media bonanza will cure cancer, while Larry Moran, strolling on the Sandwalk, develops the attack with The ENCODE data dump and the responsibility of science journalists. Ryan Gregory, from the Genomicron blog, then weighs in with A slightly different response to today’s ENCODE hype, as does PZ Myers, popping up at the Panda's Thumb, with The ENCODE delusion. Sean Eddy, at his Cryptogenomicron blog, presents a DNA-researcher's perspective by asking incredulously ENCODE says what? Finally, Ewan Birney, the bioinformatician co-ordinating the ENCODE project, presents My own thoughts at his personal blog.

Genome science reporting can only get better, and less embarrassing, from here on. However, the simple fact that several reputable science journal editors got together to orchestrate the release of the papers on the same day, thus unnecessarily delaying the publication of some of the papers (by several months), strikes me as outrageous. (Casey Bergman, at the brilliantly titled I Wish You'd Made Me Angry Earlier blog, discusses this in The cost to science of the ENCODE publication embargo.) The possibility of a media extravaganza seems to have loomed larger in the minds of the editors than did their journals' role in communication among scientists. We take them seriously, so why can't they do the same for us?


Well, that's it for this month. While you wait for the next edition, you will find the Carnival of Evolution on Facebook and Twitter, as well as at the official Carnival of Evolution blog. Past posts and future hosts can be found on the Carnival index page.

Next month's Carnival will be hosted at Sorting Out Science. You can submit posts for the next edition using the Carnival submission form (which requires you to log in), or by sending an email to Bjørn Østman.

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