The simpler cichlid: a recent adaptive radiation

If I was asked to name a few of the most compelling systems in evolutionary biology, I’d certainly start with Darwin’s Finches. Next might come peppered moths, African cichlids, stickleback, Caribbean Anolis lizards, or Lenski’s E. coli. What’s interesting about this (very short and incomplete) list is that 4 of the 6 examples represent adaptive radiations.

Adaptive radiation is when one ancestor occupies different environments and undergoes rapid phenotypic divergence to exploit the resources of those environments (for a full discussion of the topic, read Schluter 2000). Perhaps one of the reasons adaptive radiations are so well known as evolutionary examples is because, on the surface, it is conceptually quite clear how these processes may occur. However, our understanding of the actual underlying processes is still very much in progress. Continue reading

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The Fourth Reviewer: More suggestions about suggesting reviewers

Tim Vines is an evolutionary ecologist who found his calling in the process of peer review. He was Managing Editor of Molecular Ecology from 2008 to 2015, launched The Molecular Ecologist in 2010, and is the founder and Managing Editor of Axios Review. Here, Tim is The Fourth Reviewer, taking on your questions about peer review and publishing. Got a question for the Fourth Reviewer? Send us an e-mail!

Should I ask people before I recommend them as reviewers on my manuscript?

Interesting question! Getting in contact with people before listing them as ‘preferred reviewers’ has never occurred to me before, but my instinct is that this is a bad idea.

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Island-Hopping with an E.I.D.

If you live in the U.S. and feel like Zika virus is getting closer to home, that’s because it is. Although there are no known cases of Zika transmission by natural vectors in the lower 48, experts have stressed that the virus’ spread remains unpredictable. The key word is ‘remains’ because, over the past year, Zika raced through large parts of South and Central America, leaving epidemiologists scrambling to both characterize and contain it. A conspiracy theory this is not.

In last week’s edition of Science, Faria and colleagues take an essential step in the process of describing the dynamics of this emerging infectious disease (E.I.D.). They trace the recent history of Zika virus using a dataset of new and previously reported genome sequences from across its range. Their paper also includes a large smattering of data points from Brazil, where the virus reached epidemic proportions (and surging notoriety among Western media) by mid-2015.

Correlation between airline passengers from Zika-infected countries arriving in Brazil per month versus number of suspected cases of Zika in French Polynesia on that same timescale (Figure 3C from Faria et al. 2016).

Zika virus is native to Africa and southern/southeastern Asia, and its island-hopping trek across the Pacific in an America-ward direction over the past decade has been impressive.  Continue reading

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Neglected mycoplankton, no more

Taylor and Cunliffe (2016) provide a window into the world of the plankton in which they focus on a rarely studied component, the planktonic fungi (mycoplankton).

Marine mycoplankton exist as free-living filamentous and yeast forms or as parasite of other planktonic species.

© wikipedia

© wikipedia

Their roles in the pelagic ecosystem have largely been surmised by comparisons with terrestrial and aquatic analogs.

The studies to date have focused on single snapshots of mycoplankton diversity. Yet, time series data sets can be powerful tools that can enable the description of the key environmental drivers that influence planktonic communities. For example, time series of other planktonic groups, such as the bacterioplankton, have shown that there are annually repeating season-scale patterns in diversity that relate to changes in environmental parameters, such as seawater temperature or organic carbon availability.

Taylor and Cunliffe followed the mycoplankton communities at a long-term monitoring site in the Western English Channel. This site, L4, is influenced by the influx of freshwater from the Tamar and Plym rivers. It turns out that this riverine input drove mycoplankton alpha diversity. They also found that chytrid blooms matched diatom blooms over consecutive years.

 [Their] data empirically reinforce the developing paradigm that, similar to terrestrial and freshwater fungi, marine mycoplankton occupy a complex range of niches as saprotrophs, nutrient recyclers and parasites.

Mycoplankton have to be considered in order to understand the structure and function of the coastal pelagic ecosystem.


Taylor and Cunliffe (2016) Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance. The ISME Journal doi:10.1038/ismej.2016.24

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How to make the most out of your phylogenetic study

Phylogenetic studies are crucial for ecology and evolution. However, their usefulness for comparative biology or meta-analyses can vary considerably. Especially the inclusion of unidentified species (“Balanus sp.”) obstructs their use in comparative studies. How can I attach life history or morphological data collected in previous studies to an unidentified species? There is no way of telling whether Balanus sp. of one study is the same Balanus sp. of another study. In most cases, I would guess not… You see the problem?

small_tree_w_traitsI am currently working on assembling the “Open Tree of Barnacles”, which means I am obtaining published barnacle phylogenies, curate them to match current taxonomy, and then let the awesome people from the Open Tree of Life project do their tree assembly magic. During this work, I felt frustrated at times when dealing with “wasted trees”. Trees that a lot of effort and data went into, but little information comes out; namely such trees with a lot of unidentified species. These unidentified’s appear in the Open Tree of Life, but cannot be linked to species used in different studies, or the taxonomy underlying the Open Tree of Life. Moreover, such unidentified species have no value in comparative studies – one of the big goals of the Open Tree of Life project!

Here are some tips to make the most out of your phylogenetic study, borne out from my curation work on the Open Tree of Life project, and my interest in comparative biology.

Before you begin a phylogenetic study…

  • Think about including a taxonomist to help identify species and describe species discovered during the study.
  • Familiarize yourself with the current taxonomy, especially current species names.
  • Deposit specimens at museum or other official collections. Basically, make them accessible for other researchers.

While you are doing the hard work…

  • Use the same IDs throughout the study, e.g. let the same ID’s be part of the specimen ID, the sequence name and the phylogenetic tree tip.
  • Make sure sequences can be linked to tree tips as well as specimens. This will not only help you at the time of publication when you need to make tables for all these information, but allows sequences to be linked to trees, and to add more data (be it molecular or physical trait data) to certain individuals.

After the tree is made, but before you forget all about it…

  • Deposit sequences and trees in appropriate databases, e.g. sequences in NCBI’s GenBank and trees in Open Tree of Life and/or TreeBase.
  • Deposit metadata (when and where specimens were collected, how tree was generated, what kind of data are the trees based on) with the sequence and tree data, and separately in spreadsheets, which can be made available in Dryad or figshare.
  • If you identified new species based on molecular data, make an effort to describe them. Either by collaboration with a taxonomist, or by doing it yourself.

I know that describing species is hard work*, but the benefits are huge: A) You get to name a species! B) Your work will get cited because you described a new species. C) Your work will get cited because your phylogeny is now very useful for comparative studies. D) Your new species may give rise to work on their ecology or evolution – in which case your work would get cited. E) If you are anything like me, you feel frustrated by seeing unnamed things – after all, the categorization of things is a main characteristic of the biologist. Imagine the satisfaction of having this “sp.” turn into a name!

*Dear ICZN, I do not mean to encourage the rogue naming of taxa that may not be “real” species. However, I have come to the conclusion that naming species would allow us to start the discussion on whether a species is real or not. Without a name, we do not have common grounds for discussion. Therefore, hail to the naming of species, and to making this process easier!

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The Molecular Ecologist Summer Meetings Round-up


Summer conferences are some of the best places to get up-to-date with your field, meet new collaborators, and hatch new ideas. The Molecular Ecologist contributors will be out in force this year, and we’d like to meet you!

Below you will find a list of all the various meetings that contributors will be attending this summer. Whether you have an idea for the blog, wrote a new paper you want to discuss, desire one of those sweet mugs, or want to do a guest post yourself, contact us via the “contributors” section on this page and let’s chat!

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New branches on the tree of life


(Trees from Darwin (1837), Haeckel (1866), and Woese (1990))

We’ve come quite a long way since Darwin sketched out his tree in 1837 connecting, with branch tips representing animals and microbes currently in existence and branches and trunks their ancestors. The most recent tree of life was revealed yesterday in Nature Microbiology, the latest and most extensive view of biodiversity on the planet.

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Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, phylogenetics | Tagged , , , , | Leave a comment