Evolution 2018 Day 1: From genomics in the wild, to new models of selection

It’s Evolution conference time! Evolution has long been my favourite fixture in the conference calendar, with its diverse mix of theoretical and empirical studies that span the full range of evolutionary biology. This year it’s the second Joint Congress on Evolutionary Biology, which brings together the European Society for Evolutionary Biology, the American Society of Naturalists, the Society for the Study of Evolution and the Society of Systematic Biologists all under one roof in the lovely city of Montpellier in the south of France.

The conference kicks off with the ESEB Presidents’ Award delivered by Loeske Kruuk (Australian National University), with a talk entitled ‘Evolutionary dynamics and fitness in wild populations’. Studying quantitative genetics in the wild is challenging because many classical theoretical predictions don’t apply, and because robust inferences require long-term studies that genotype complete populations. Loeske discusses how her work generating a completely pedigree, along with large-scale phenotypic data, for the superb fairy-wren (Malurus cyaneus), has given insights into quantitative genetics in the wild. Interestingly she shows temporal covariance between body size and fitness, but this is because body size is related to other traits, and therefore there is no expectation of body size showing an evolutionary response. She also shows date of moult is heritable, and suggests this means that ‘the early bird gets the girl’. She finishes up by saying that there are less than 10 estimates of fitness for wild populations, and that there are some consistent effects between species (like cohort effects) but lots of variation. I’m really looking forward to seeing the paper where these comparisons of fitness are presented.

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Posted in adaptation, community, conferences, evolution, genomics, population genetics, speciation, theory | Tagged , , | 1 Comment

For flexible eDNA analysis, just capture whatever you want

This is a guest post by Taylor Wilcox and Katherine Zarn, whose article “Capture enrichment of aquatic environmental DNA: A first proof of concept” is online ahead of publication at Molecular Ecology Resources. Wilcox and Zarn wanted to elaborate on the usefulness of capture enrichment as an alternative to metabarcoding beyond what they could cover in that paper’s discussion, and this post is the result. — JBY

Environmental DNA sampling for multi-taxa species detection (i.e., the inference of species presence from genetic material in the environment) has been a hot topic lately. Some of the most exciting recent work has used high-throughput sequence (HTS) to simultaneously screen for the presence of large suites of taxa (Valentini et al. 2016), estimate relative species abundances (Ushio et al. 2018), and even make inferences about population structure (Sigsgaard et al. 2016). Most of these studies have relied on metabarcoding, which despite its obvious utility, has some real limitations. One fundamental limitation emerges from a reliance on shared primers for bulk amplification of mixed templates. This tends to generate skewed relative sequence abundances after enrichment and potential loss of species detection (Deiner et al. 2018, Piñol et al. 2018).

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Posted in community ecology, DNA barcoding, metagenomics, methods | Tagged , | 1 Comment

Transcriptome sequencing catches bats' immune systems napping

A little brown bat (Myotis lucifugans) infected with the white-nose fungus. (Flickr: US Fish and Wildlife Service)

Populations of multiple North American bat species have been more than decimated by white-nose syndrome, a fungal disease that spreads within roosting colonies and becomes deadly during hibernation. A paper just released online early at Molecular Ecology adds support to a hypothesis that the reason for the fungus’s virulence is that hibernation puts bats’ immune systems to sleep — and waking up to fight the fungus costs more than they can afford.

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Just So Stories addendum: How the stickleback keeps getting its stickles

Model organisms have been essential tools for genetics research since the field was formed.  Kelle Freel discussed the characteristics that make for a good model organism in a previous TME post.  Briefly, traits like short generation time, lots of offspring, and easy-to-track developmental stages have been exploited to answer questions about molecular mechanisms behind transmission, cyto-, developmental, population and quantitative genetics and comparative genomics.  A lesser-known model organism is the three spined stickleback, Gasterosteus aculeatus (though it has been mentioned or discussed in several previous TME posts).

Why? Because this fish has the rare honor of being an evolutionary and ecological model organism.  Sticklebacks occur holarctically in marine, estuarine, and freshwater (freshwater) habitats in Europe, Asia, and North America.  During the last retreat of the glaciers in the Pleistocene, this historically marine species began to invade freshwater habitats many times on different timescales in different places. What piqued researchers’ interests about these fish, in the pre-genomic age, was the striking phenotypic variation in various newly-formed freshwater populations and how quickly these divergences happened.  Even though freshwater morphs can differ markedly from each other, even in the same lake, there are certain morphological changes that consistently happen in the evolution from marine/anadromous to freshwater forms, like the loss of body armor.

Fig 1 from Cresko et al 2004. A-C) are freshwater-derived representatives while D) is an anadromous specimen.
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Robin Waples awarded the 2018 Molecular Ecology Prize

The 2018 Molecular Ecology prize has been awarded to Robin Waples for his work on conservation biology and management, particularly as the leading expert on approaches for using molecular markers to estimate and understand effective population size in natural populations, including subdivided and continuously distributed populations, and use of time series analyses. His studies of populations with overlapping generations have illuminated the evolution of life-history changes in species that are harvested by humans, and made important contributions to understanding fisheries populations. By adapting population genetic models to real-life situations, including structured populations with gene flow, and developing statistically rigorous analyses, his contributions have significantly advanced both conservation and evolutionary ecology.

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They joy of genome sequencing: when genomics meets natural history

When I have a massive pile of papers that I need to read, I can’t help but look at the ones with interesting natural history first. There’s something exceptionally satisfying about using modern tools to dig deeper into the features that make each species so interesting. Many molecular ecologists, myself included, started a career in biology because of a love of natural history, and I think it’s great when this passion can be captured in modern research. One area where an understanding of an organism’s natural history is perhaps surprisingly important is in whole genome sequencing. While it’s becoming increasingly common to sequence, assemble and annotate genomes (though I’d still argue it’s challenging to do it well), many papers do more than just generate a genomic resource, and relate genomic variants to unique properties of a species. Even better is when these interesting features of a species can be related to other experimental work, or sequencing additional natural populations, to gain deeper insights into organismal biology.

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The eyes have it!

Eyes are pretty darn complicated, which makes them cool models for studying complex trait evolution.  Maybe the first time I realized how interesting eyes are when I saw this by the oatmeal about the amazing-ness of the mantis shrimp (are they your new favorite too?), or when I first listened to Colors (or the update) by Radiolab (which also mentions the majestic and clearly magical mantis shrimp).

Graphical Abstract (Picciani et al., 2018).


Eyes exist at different levels of complexity, at their most basic they might have some photoreceptors, pigments, or maybe even lenses or mirrors. As Picciani et al., (2018) from the Oakley lab at UC Santa Barbara, point out, many researchers focus (no pun intended) on the evolution of eyes in bilaterian animals, essentially the animals that have a right and left side (like us). As you might imagine, these visual systems are incredibly intricate, and unraveling their evolution is quite the challenge.
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Metabarcoding for every body, every habitat, every time

The immediate reason why I wanted to write about Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles is its usefulness for the scientific community and the effort of the authors to make their study reproducible. All their code and data are online and publicly available. It was even accessible before the paper got accepted!

Secondly, I like observing how the field of metabarcoding eukaryotes is developing. I feel at home in the field of metabarcoding prokaryotes, that is archaea and bacteria. Hence, many of the approaches are familiar. People who study prokaryotes and very small eukaryotes could not just go out and observe their objects interacting in the wild. Because these tiny microorganisms are difficult to see. One very successful way to work around this obstacle was to use genetics and study microbial DNA instead. The 16S rRNA gene has become extremely useful to bacteriologists. This gene is part of the prokaryotic ribosome. It is a very essential gene – most prokaryotic organisms have it. Highly conserved regions of this genes serve as primer binding sites for universal primers and variable regions in between them can be used to reconstruct bacterial phylogenies. 16S amplicons give us a glance at the distribution of bacteria and archaea, the oldest, most diverse and abundant species on this earth (more about this here). Most environments, from remote volcanic hot springs to human genitalia have been characterized using next-generation sequencing of 16S amplicons. While most people refer to it as 16S amplicon studies, it is basically a form of metabarcoding. Eukaryotes have a similar gene, the 18S. Hence, people studying small eukaryotes like fungi and protists have been using 18S amplicon studies for the same purpose.

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Posted in bioinformatics, community, community ecology, DNA barcoding, fieldwork, metagenomics, next generation sequencing, phylogenetics, R | Tagged , , , , , , | 1 Comment

Support the Molecular Ecologist with all-new evolution and ecology-themed merch!

We don’t often make a big deal about it, but The Molecular Ecologist has long offered merchandise for purchase to help cover our operating expenses, which are chiefly web hosting and small stipends for contributors. The platform we’d used for that was less than ideal, though — and we’ve finally set up shop on Redbubble, which offers a wider range of products at better pricing.

Molecular Ecologist-supporting shirts, images by Redbubble


You can now purchase our “heliboot” logo on a wide array of apparel, mugs, and other accessories, get a poster print of the Molecular Ecology Flowchart, or pick a side in the eternal struggle between genetic drift and natural selection. Prices start at less than $20 for a tee (before shipping and sales tax), and all proceeds benefit the blog — so check out the whole range.

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Population genetic simulation … in Lego

Julien Yann Dutheil, of the Institut des Sciences de l’Évolution de Montpellier, has a long track record of work in population genetics and genomics methods, particularly in the C++ programming language. He recently posted a video to YouTube, though, which suggests he’s trying out a new simulation platform: Lego bricks.

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