Evolutionary Biology Online Journal Club


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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


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Season 2, Meeting 4: Ecological Speciation

Join us Monday, March 18th at  4:30pm EST

Ecological speciation is a surprisingly broad topic (by which I mean picking a paper wasn’t as easy as I thought it might be…).  Schluter (2009, Science) argues there is good reason for this, as he categorizes all speciation events into only two broad categories: mutation-order and ecological.  Given that ecological speciation can just be thought of as “divergence [that] is driven by divergent natural selection between environments” (Schluter 2009), I thought it might be useful to consider a variety of mechanisms of selective reproductive isolation, or ecological speciation.  One obvious one of course is geographic reproductive isolation, which we discussed in Meeting 3, The Geography of Speciation.  So I chose a paper by Andrew Hendry, Patrick Nosil, and Loren Rieseberg, which I think does a pretty good job of providing not only different mechanisms of ecological speciation, but covers a variety of taxa, all from the premise that “adaptation to new ecological environments can cause the contemporary evolution of reproductive isolation” (Hendry, Nosil and Rieseberg, 2007).  I hope this leads to an interesting discussion!  Below is a link to the discussion paper, as well as to two other interesting review papers on ecological speciation by Schluter (2009) and Rundle and Nosil (2005), in case you have that elusive ‘extra’ time. If you have even more extra time, there was a whole special issue on ecological speciation in the International Journal of Ecology in 2012, also linked below. Hope to see lots of you on Monday!

The paper we will be discussing:

Hendry, A. P., Nosil, P. and Rieseberg, L.H. 2007. The speed of ecological speciation. Functional Ecology, 21(3): 455-464. DOI: 10.1111/j.1365-2435.2007.01240.x

Other papers that may be of interest:

Schluter, D. 2009. Evidence for Ecological Speciation and Its Alternative. Science, 323(5915): 737-741. DOI: 10.1126/science.1160006

Rundle, H.D. and Nosil, P. 2005. Ecological Speciation. Ecology Letters, 8(3):336-352. DOI: 10.1111/j.1461-0248.2004.00715.x

Special issue on Ecological Speciation, in the International Journal of Ecology (2012)

Reminder:

As usual, our meeting will be in Google+ hangouts, so here are a couple useful resources:


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Season 2, Meeting 2 – Consistency & Consensus in Taxonomy

After last session’s discussion on species concepts/definitions, people thought it might be worthwhile talking about species from a taxonomist’s point of view. There aren’t many papers I know of that talk about the taxonomic process, but if people have questions I’ll be happy to answer what I can from my experiences.

However, I did find a paper that I think does a good job of discussing some of the issues that were brought up last time, and introduces a few more ideas on what a species is from a taxonomists viewpoint, and how that viewpoint differs between individuals:

Vane-Wright, R.I. 2003. Indifferent Philosophy versus Almighty Authority: on consistency, consensus and unitary taxonomy. Systematics and Biodiversity 1 (1): 3-11. doi:10.1017/S1477200003001063 (PDF here)

Vane-Wright refers back to a short commentary that was published in Nature a few months prior that might also be of interest:

Godfray, H.C.J. 2002. Challenges for taxonomy. Nature, 417: 17–19. doi:10.1038/417017a (PDF here)

Anyways, Vane-Wright discusses the nomenclatural plight of a group of African butterflies and how definitions of the species of interest have changed through time and with differing research opinions/objectives. Everything from creationism to cladism is discussed, and the author proposes a new hierarchical system that only serves to complicate matters in my mind. I think it should be a pretty interesting discussion, and I’m looking forward to hearing what everyone else thinks of it.

P.S. There was some discussion about how taxonomy can affect conservation last time as well, so I thought I’d point people to this paper which does a nice job of discussing the issue:

Mace, G.M. 2004. The role of taxonomy in species conservation. Philosophical Transactions of the Royal Society B: Biological Sciences 359: 711-719. doi:10.1098/rstb.2003.1454 (PDF here)


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Species Concepts for Conservation – Nature 494

As if on cue, Nature published a short Correspondence letter this week which talks about the effect that species splitting is having on mammal conservation. You can read it online here (paywall, so also here).

Personally, I don’t really like it when someone says we should be stemming our research to fit political ideals, and feel that the authors are just trying to get other taxonomists to conform to their own ideas of what a species is. It is interesting to see how the Biological Species Concept is pitted against Phylogenetic Species Concepts however, and it’s clear that some people are not as open to hybrid definitions/concepts like we discussed earlier this week.

What do you think? Should we restrict changing species concepts of threatened species, or are there other ways to approach this problem without throwing taxonomy under the bus?
Zachos F.E. (2013). Taxonomy: Species splitting puts conservation at risk, Nature, 494 (7435) 35-35. DOI:


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Paper summary – de Queiroz 1998

I managed to volunteer myself to lead the first discussion for Season 2, so thought I would write down a brief summary of the paper and a few of my thoughts on it as a spur to conversation. If you haven’t caught up with it, here’s the details of the paper we decided on for the first session

de Queiroz, Kevin. “The general lineage concept of species, species criteria, and the process of speciation.” (1998). in  Howard, Daniel J., and Stewart H. Berlocher, eds. Endless forms: species and speciation. Oxford University Press, USA, 1998.

There are many species concepts, but one definition?

Everyone who has done an undergraduate course in biology has had the “species concept” discussion. Although species are fundamental units in biodiversity, and often the natural unit of comparison in evolutinary and ecological studies, bioloigsts spend quite a lot of their time arguing about exactly what constitutes a species. John Wilkins, who knows a thing or two about the debate, lists 26 species concepts that have at least one supporter. de Queiroz provides a summary of the more popular concepts, and the evidence they use to delimit species.

The huge number of species concepts available seems at first to be a barrier to the important tasks of delimiting species (alpha taxonomy) and working our how they came to be (the study of speciation). But, de Quieroz argues, all these concepts can be shown to share a single definition of species, and only differ in determining the types of evidence we should look to in deciding if a population fits that definition:

All modern species definitions either explicitly or implicitly equate species with segments of population-level evolutionary lineages.

For de Quieroz a species is a population, held together by some force, evolving through time, and all the existing species concepts already recognise this idea. In sexually reproducing organisms, it is reproduction itself that can pull partially-isolated populations in a single direction. de Quieroz doesn’t suggest similar forces that might apply in asexual species, but notes existing species concepts for these species presume such forces exist.

Linking species status to the speciation process

For me, the strongest and most interesting part of the general lineage species concept (GLSC) is the way it brings what we know about speciation, the study of the origin of species, into taxonomy, the process by which we identify and describe species. de Quieroz illustrates a hypothetical speciation proceeds something like this (this is actually my version, lifted from a powerpoint slide, so blame me if it’s misleading):

The point here is not the speciation will allow follow this path, but that speciation is fundamentally a process  not an event, and the criteria required to fulfill various species concepts will accrue during that process. The choice of a species concept may depend on exactly what is being studied, and a more general approach to taxonomy should take all the evidence available.

Some thoughts

This paper is now 15 years old, and the ideas it contains have had a large impact on both speciation research and taxonomy (it’s been cited almost 600 times). I’m sure we’ll have no shortage of things to talk about, but here’s a couple of things that nag away at me when I think the GLSC is the answer to all our problems

Applicability outside of living metazoans
I only work on animals that are alive today. Can the GLSC be applied to asexual populations, or species that arise from hybridisation rather than simple splitting of lineages?Can we apply the GLSC to extinct species, where it’s very hard to know anything about the populations  from which fossils come, and members of the same lineage could conceivably be separated by millions of years of evolution?
Have we really embraced the GLSC
For me,one of the major lessons of the GLSC should be to stop fighting over th One True Species Concept, and instead focus on gathering evidence that allows us to determine if populations are evolving independently. This idea is paid a lot of lip-service, but in practice species delimitation studies rely heavily on phylogenetic and population genetic methods. Is this really integrative?