Experimental harvesting reduces gene expression variation

Human activities represent unique selective pressures for natural populations. This is especially true for fish species where we routinely harvest individuals from the wild, i.e., through fishing. It has been recognized for some time that overfishing can result in population crashes. More recently it has become clear that selective harvesting can result in evolutionary changes. For example, by fishing only large individuals there is selection to reach maturity at a younger age and smaller size and to direct more resources towards reproduction. For a review of fisheries induced evolution, see Heino et al., 2015.

An interesting (depressing?) phenomenon in fisheries is the lack of recovery of many populations even after the cessation of fishing. Atlantic Cod provide a prime example of this issue. In the Gulf of St. Lawrence, the population initially collapsed in the 1980’s and fishing was largely stopped in 1993. However, the fishery has still not recovered (Swain et al., 2007), perhaps, in part, due to fishery induced evolution.

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Non-model organisms are so hot right now

Zoolander image courtsey of wikicommons

What makes a model organism? Well, as the name suggests, they are widely studied and have been adapted to a vast array of common genetic techniques. A few of the most often utilized organisms, which you are most likely already (at least) vaguely familiar with, include Drosophila melanogaster (the fruit fly), Escherichia coli, Saccharomyces cerevisiae (the yeast everyone thanks for bread, beer, and vino), Caenorhabditis elegans (everyone’s favorite nematode), and Danio rerio (the zebrafish). Model organisms are often easy to work with in a lab and easily manipulated genetically.

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How Molecular Ecologists Work: it’s back and we need your help

Molecular Ecologist contributors are hard at work behind the scenes filling out a busy fall of new posts. Part of the renewed push includes a new season of “How Molecular Ecologists Work”, a chance to sit down at the desks of our colleagues and see their approaches on productivity. Along the way, we picked up on a few dozen helpful tips, saw offices that varied from coffee shops to beautiful views, and learned that no one actually believes they are all that productive.

The response to last year’s interviews were fantastic, and it was clear that the readers of this blog have an intense curiosity for the details that make up our daily work, whether it be in the lab, out in the field, or at a computer terminal. However, it was clear that How Molecular Ecologists Work was biased towards the United States. This might not be surprising since most of us contributors are based at US universities (spatial autocorrelation?), but we can do better profiling molecular ecologists from across the world.

This is where you come in. Take a look at series 1 of How Molecular Ecologists Work, then ask yourself: Do I admire an international scientist and want to know more about how they work? If you do, contact me (robert.d.denton@gmail.com)!

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The largest mammalian genome is not polyploid

Some 40 million years ago in South America, following the arrival of the common ancestor of caviomorph rodents from the Old World, big changes were afoot.

Specifically, the caviomorph colonists were beginning to give rise to an extant evolutionary progeny of nearly 250 species and 13 families of endemic South American rodents, which show notable diversity in morphology, ecology, and life history (think New World porcupines, chinchillas, and guinea pigs). Interestingly, caviomorphs are also the bearers of notable genomic changes (i.e., evolution of genome size and structure; like the number, form, and arrangement of chromosomes). Functional numbers of chromosomes vary widely from 10-118; moreover, the most extreme instances of genomic evolution in caviomorphs tend to be found in clades with highest diversification rates. That pattern (correlated rates of speciation and genomic evolution) is not uncommon in mammals, and its presence in caviomorphs reiterates persistent holes in our understanding of the links between genomic evolution, speciation, and molecular adaptation.

Present (and prominent) within this milieu of caviomorph chromosomal combinatorics is a species named Tympanoctomys barrerae, or the red vizcacha rat (Figure 1). Red vizcacha rats are small rodents (if you’re a North American desert dweller, think kangaroo rat size) that inhabit the high-latitude, cis-Andean deserts of western Argentina, where they eke out a living largely on low-hanging saltbush fruits. Amazingly, the cells of T. berrarae host nuclear genomes that are more than double the size of an average mammal, and nearly three times that of the human genome. This mass of DNA is packaged into a whopping 102 chromosomes that, while failing to comprise the largest known mammalian karyotype (an honor that belongs to the Bolivian bamboo rat), are still double that of most of its closest living relatives. Possession of the largest known mammalian genome is plenty sufficient for status as an ‘evolutionary curiosity’; however, there are still major questions related to how and why the red vizcacha rat’s genome became so large.

“Evolutionary relationships, chromosome number (2n), and genome size in picograms (C-value) of vizcacha rats and other members of the family Octodontidae (left). Red vizcacha rat T. barrerae in El Nihuil, Mendoza, Argentina (photo credit: Fernanda Cuevas).” Caption from Evans et al. 2017.

In a new paper in Genome Biology and Evolution, Ben Evans, Nate Upham, and colleagues bring whole-genome and whole-transcriptome data to bear on those questions. Their analysis compares and contrasts genomic properties of T. barrerae with those of one of its closest relatives, the mountain vizcacha rat (Octomys mimax). Geologically speaking, these 2 lineages are relatively recently diverged (earliest Pliocene), but the genome of the red vizcacha rat is still twice as large and comprised of nearly double the number of chromosomes. It is worth noting that new specimens of T. barrerae were collected specifically for this work, hard-fought during recent expeditions to the Argentinian high desert. (That part of the study is nicely chronicled here, allowing lots of room for vicarious experience!).

Evans et al. use a variety of tests to understand whether red vizcacha rat genome expansion might be the result of whole genome duplication (polyploidy is extremely rare in vertebrates), but also if accumulation of repetitive elements may have played a role. As an experimental control in the test for polyploidy, the authors subjected genomes of 2 African clawed frogs (Xenopus; 1 of which is a confirmed tetraploid) to the same battery of tests.

The preponderance of their results reject polyploidization in T. barrerae, instead suggesting significant accumulation of repetitive regions as the cause for genome expansion. Interestingly, however, only a few of the repetitive elements BLAST to regions of known biological function in related rodent species. The rest either find their match in regions of unknown function (satellite or micro satellite DNA) or simply lack a clear match at all. According to the authors, their results “support that 1) [the genome of T. barrerae] evolved by expansion of a diverse mosaic of repetitive sequences, and 2) the genomic distribution of these elements is not uniform.”

Still an open question is whether these repetitive genomic elements serve actual biological function(s), and whether those functions were involved in the speciation process. One hypothesis is that the repetitive regions (which make up a whopping 1/2 of the genome of T. barrerae) are somehow involved in adaptation to desert environments and processing of desert food sources. T. barrerae inhabits regions of high-latitude South America that, due to a sizable Andean rain shadow, receive among the lowest rainfall of anywhere in the New World. The species has also evolved an ability to survive on diets made up largely of saltbush fruits. Continuing to pinpoint the causes and consequences of genome expansion in T. berrarae will likely teach us much more about genome evolution, adaptation, and diversification and their links in endemic South American rodents.

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Genomes are coming: Sequence libraries from the honey bee reflect associated microbial diversity

One of the coolest of reasons that cheap sequencing is nifty, in my opinion, is that it has allowed researchers to study individual eukaryotic organisms, and their associated microbes (their microbiome). Let’s be real, we are in the midst of identifying essential interactions between eukaryotes and their microbes, which are key in driving evolution. If you’ve any doubt about that, feel free to check out this great read, or take a glance at this article.

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Posted in Coevolution, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing | Tagged , , | Leave a comment

TME Chat: That #NewPI life

This post is a new format for The Molecular Ecologist: a group chat. Sometimes there are multiple TME contributors who have interesting takes on the same topic, and it’d be nice to hear from them all, and sometimes a conversation is better than a formalized essay. We’re trying this out with a chat about life as new PIs — two of the regular TME contributors are starting their second year as tenure-track faculty, and I’m about to start my first. So we got together on the TME Slack channel to talk about that #NewPI life for an hour. What follows is a transcript of our chat, lightly edited for clarity and grammar and with the odd hyperlink added for context. Enjoy!

— Jeremy

Jeremy Yoder: Hi, everyone! The last year or so has seen some major career transitions for TME contributors — including, now, three new professorships. Stacy Krueger-Hadfield and Arun Sethuraman both started tenure-track positions in the last year, and I’m getting read to move to Los Angeles to start my own. So it seemed like a good time to round up the three of us for a chat about life as new PIs. As the newest one, I’ll mostly moderate and ask questions. Honestly, I want to know everything Arun and Stacy can tell me about getting started.

Let’s start with full introductions: your career stage, a little about what you do, scientifically, and the campus and department where you’re faculty. Maybe Stacy first?

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This new review explains why soft sweeps are the bane — and the baseline — of ecological genetics

(Flickr: andrew)

If you’ve done ecological genetics research in the last decade, you’ve almost certainly cited a series of papers by Pleuni Pennings and Joachim Hermisson, which broke down the problem of soft selective sweeps. Pennings and Hermisson have revisited soft sweeps in a big, detailed new review article for Methods in Ecology and Evolution, which pulls together more than a decade of research following the original studies, and makes a good case that everyone’s favorite excuse for a less-than-dramatic genome scan result is not going away any time soon.

First, what exactly is a soft sweep? Well, it’s a selective sweep that is … not hard. The original papers addressed a couple different ways that natural selection might fail to produce the classic signature of a “hard” selective sweep — in which a single advantageous genetic variant spreads through a population over a few generations, eventually becoming the only variant present — but didn’t quite line them up for comparison. In the new review, Hermisson and Pennings do this very explicitly.

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