Evolutionary Biology Online Journal Club


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#EBJClub 2.6 – Is regional species diversity bounded or unbounded?

Today’s meeting will be through Google+ hangouts, so here are a couple useful resources:


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Last meeting for Season 2 – and a EBJClub/PEGE crossover!

Hey everyone!

Sorry for the very delayed post, this has been a hectic end of semester to me. I was supposed to choose the next paper for discussion on something related to sexual selection and speciation, but I think we’ve figured out something cooler to do!

Lynsey McInnes (@McLynsey) and Will Pearse (@willpearse) have been running the very, very cool PEGE (Phylo-Eco-Geo-Evo) Journal Club since early this year. It follows a format that is a little different than our EBJClub: they choose a paper to thoroughly review and comment on in their webpage, creating a really nice archive of their impressions of these papers, while at the same time conveying their importance and main points in a very accessible way to those interested. They also have guests come from time to time and choose a paper, contributing to the dialogue. It’s really great and I’ve learned a lot from reading their posts – you should definitely check it out!

So you can see that the goal of PEGE and EBJClub are similar – promote the reading and discussion of important topics in evolutionary biology among students and researchers that don’t necessarily share (anymore) the same lab -, but we have ended up with quite different ways of doing so, which is interesting of itself. I had known of their journal club for a while and had been following their posts, but a couple of weeks ago it kinda clicked on me – “hey, we should do something together!”

So I contacted them and here we are! Lynsey and Will were kind enough to accept my invitation, choose our next reading and will be joining us for the next discussion! At the same time, PEGE will have a post on the same paper, which should help anticipate some of the issues and questions we might have, as well as highlight interesting topics that are worth discussing in the Google Hangout.

The paper chosen is a recent Biology Reviews article by Howard V. Cornell titled “Is regional species diversity bounded or unbounded?”. Don’t let the title fool you – it might seem kinda specific, but a quick read of the abstract will show that this paper brings together many (perhaps all?) the main topics we have discussed throughout the semester, and really is a perfect way to wrap up the discussion on speciation and biological diversity!

As is usual for Biology Reviews papers, this paper is long, conceptual and thus might require a good, careful read to take the most out of it. Therefore, I am suggesting we meet Monday, May 15 13 at our usual 4:30 EST time slot to discuss it – leaving a good 10 days to go over the paper.

Does that sound good? I’m excited, and I can’t wait to see how it goes!

Howard V. Cornell (2013) Is regional species diversity bounded or unbounded? Biological Reviews 88:140-165.

Abstract. Two conflicting hypotheses have been proposed to explain large-scale species diversity patterns and dynamics. The unbounded hypothesis proposes that regional diversity depends only on time and diversification rate and increases without limit. The bounded hypothesis proposes that ecological constraints place upper limits on regional diversity and that diversity is usually close to its limit. Recent evidence from the fossil record, phylogenetic analysis, biogeography, and phenotypic disparity during lineage diversification suggests that diversity is constrained by ecological processes but that it is rarely asymptotic. Niche space is often unfilled or can be more finely subdivided and still permit coexistence, and new niche space is often created before ecological limits are reached. Damped increases in diversity over time are the prevalent pattern, suggesting the need for a new ‘damped increase hypothesis’. The damped increase hypothesis predicts that diversity generally increases through time but that its rate of increase is often slowed by ecological constraints. However, slowing due to niche limitation must be distinguished from other possible mechanisms creating similar patterns. These include sampling artifacts, the inability to detect extinctions or declines in clade diversity with some methods, the distorting effects of correlated speciation-extinction dynamics, the likelihood that opportunities for allopatric speciation will vary in space and time, and the role of undetected natural enemies in reducing host ranges and thus slowing speciation rates. The taxonomic scope of regional diversity studies must be broadened to include all ecologically similar species so that ecological constraints may be accurately inferred. The damped increase hypothesis suggests that information on evolutionary processes such as time-for-speciation and intrinsic diversification rates as well as ecological factors will be required to explain why regional diversity varies among times, places and taxa.

Keywords:
adaptive radiation carrying capacity coexistence diversification niche
niche conservatism phylogenetics saturation species-area species diversity species-energy


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“World’s First Online Journal Club”

Today Morgan Jackson alerted us to a recent piece in the journal Nature entitled “Online journal club” (Nature 496, 261 – 11 April 2013 – doi:10.1038/nj7444-261c). The main thrust of this short “Career Brief” article is that another group called Fertility and Sterility has recently stated up an online journal club using a platform called Journal Club Live™ (http://journalclublive.com/). This website has created the “world’s first online Cyber-Journal Club™ platform”, which basically does the same thing as we have been doing with G+ Hangouts™ and YouTube™. Devin Drown rightly pointed out that this short blurb in Nature reads like an advertisement for  Journal Club Live™.

I think for most of us the headline in Nature was both exiting and disheartening. We are all happy to see the idea of an online journal club approach gaining more general interest, but it is disappointing to see the high-profile exposure gained by another group for doing essentially the same thing that we have been doing since September 2012 (https://evobiojournalclub.wordpress.com/2012/09/).

However, since September we have grown and matured as a group. We have overcome issues relating to technology, topic selection, discussion format and more. I think we all see the inherent value of an online journal club, and I also see us as people who are uniquely positioned to write a piece on the topic. A few of us have decided that it is worth trying to publish a short paper that explicitly spells out the value of online journals clubs, and the practical steps to implementing one.

If you have any suggestions or comments that you think might be relevant for this paper please feel free to add them in the comment section below. Specifically, what do you think should be in this paper? What are the main strengths & weaknesses of online journal clubs? What are the main technological challenges that need to be overcome?


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Food for thought: geography as (just another) isolating mechanism

Hey everyone, I thought I’d post this here as it might be interesting to us. I mentioned this paper briefly in the last discussion, and though it might be too theoretical for our group (though I am open to have that questioned), I thought some thoughts in here would be helpful to us.

So even though I think we have mostly agreed that while interesting, focusing too much in geographical aspects of speciation (sympatry/parapatry/allopatry) as very crucial can be distracting, and confusing if treated as an alternative hypothesis to other processes (such as ecology) driving diversification. Nonetheless, we keep on coming back to this topic, and I started wondering if it could be just because we lacked a more formal framework that we could have to substitute the one we’ve been exposed to so far.

I was reading a paper by Mark Kirkpatrick and Virginie Ravigné (Speciation by Natural and Sexual Selection, The American Naturalist 2002 159:S22-S35) and I think they might offer just that. In the paper, they list five conditions necessary to speciation via selection (natural or sexual), of which the second one, “A Prezygotic Isolation Mechanism”, deals with the element of geography. From the paper (emphasis are mine):

Here again there is the opportunity to unify models of speciation. Assortment and mating preferences can be treated as a single form of prezygotic isolation by regarding assortment as the special case where a mating preference acts on itself.

The Geographical Setting

One of Mayr’s great legacies for our understanding of speciation was his emphasis on the importance of biogeography (Mayr 1963; see Coyne 1994). As a result, the geographical context of speciation—the allopatry versus parapatry versus sympatry continuum—is traditionally viewed as the most important factor in speciation (table 1, sec. II.C).

Our list of fundamental elements for speciation can be simplified, however, if we view geography as simply another form of assortative mating. Consider geography as a genetic locus. Each geographical location then represents a different allele. Migration is replaced by a form of frequency‐dependent mutation at the geography locus; movement between populations is equivalent to mutation of both alleles at the geography locus. That locus enforces the most extreme form of assortative mating since only individuals that carry the same allele at the geography locus are allowed to mate.

The evolutionary dynamics of a population with this form of assortative mating are exactly equivalent to those of a geographically structured population. Although this equivalence may at first seem obscure, it is useful for three reasons. First, it shows that we can simplify thinking about speciation by treating geography as just one more type of assortative mating; geography does not need to be modeled separately.Second, allopatry and sympatry do not need to be treated as qualitatively distinct situations. Third, the correspondence between geography and assortment helps make clear why allopatric speciation is so powerful and so prevalent: it is an exceedingly accurate form of assortative mating. Very few other types of assortative mating guarantee that only individuals carrying the same allele at a single locus will mate together. Combining this with ubiquitous spatial variation in selection produces a potent engine for generating new species. It may well be critical to the great majority of speciation events, as argued by Mayr (1963).

Although this might seem like just a “modeling trick”, I think the conceptual basis for it can be very helpful: we can view allopatry as a mechanism of prezygotic isolation with a behavior very similar to other possible mechanisms, with the important notion that it can (quite commonly) be a very strong one.

To me, this makes it very clear that geography can be one of many mechanisms of isolation, that it can act in concert with other occurring mechanisms, and most importantly, it needn’t be treated as an “alternative hypothesis” to ecological speciation. Ecology can play a role in many of the five conditions listed by Kirkpatrick and Ravigné; in some cases it might reinforce other prezygotic barriers (including geographical ones), in others it might weaken them, and in other cases it might just affect other of the conditions to speciation, that do not relate to prezygotic barriers. I think this can help deal with much confusion in the topic.

Well, these are my thoughts, would love to hear what you have to say!


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#EBJClub 2.5 – Genetics of Speciation

Today’s meeting will be through Google+ hangouts, so here are a couple useful resources:


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Season 2, Meeting 5: The Genetics of Speciation

On Monday the 1st of April, at 16:30 EST, we’ll be discussing some elements of the genetics involved in the speciation process between two flycatcher species (not an April Fool’s joke, I promise).

After the last meeting, I looked for papers that explained the genetics of speciation in a relatively simple and clear language, all the while focusing on one example. From this search comes the following review:

Saetre, G.-P., & Saetre, S. A. (2010). Ecology and genetics of speciation in Ficedula flycatchers. Molecular Ecology, 19, 1091-1106. doi: 10.1111/j.1365-294X.2010.04568.x

The authors first explain why the pied and collared flycatchers provide an interesting study model. Then, they go on to answering the question of “what is keeping them apart and how did such barriers evolve” (even though they do hybridize in some areas of their distribution) by describing the various genetic factors that reduce the gene flow between the two species.

As an optional read, here is a more recent paper, which was suggested by Rafael, on the genomic landscape of species divergence in the same birds:

Ellegren et al. [there’s just too darn many authors] (2012). Genomic landscape of species divergence in Ficedula flycatchers. Nature, 491, 756-760. doi:10.1038/nature11584

Screen shot 2013-03-29 at 16.13.31