Are genetic drift and inbreeding the same thing?

Does it ever happen to you that the more you try to understand something, the more difficult to understand it turns out to be? Recently, I’ve had such a problem with two of the very basic microevolutionary phenomena – genetic drift and inbreeding.
Genetic drift and inbreeding are associated with changes in allele frequencies and heterozygosity, and are particularly important in small populations. Their causes and effects are so intertwined that I ended up asking “Are genetic drift and inbreeding the same thing?”
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Posted in conservation, evolution, population genetics, quantitative genetics, theory, Uncategorized | Tagged , , , , , | Leave a comment

Annotations on a tweet-storm directed more-or-less towards Neil deGrasse Tyson

tyson
So, Saturday afternoon, while I really should have been working on other things, this happened:


What the heck is going on here? Well, it might be obvious if you’re connected to the biology-oriented end of Science Twitter, but there’s a lot of context, and science, behind that tweet. And it’s occurred to me that it might be useful to put it all in one place, and provide some additional information that can’t be packed into even a series of 140-character snippets.
Believe it or not, it all started last Friday, when astrophysicist and popular science demigod Neil deGrasse Tyson tweeted:


Anyone with much background in biology knows this is false on its face, since there are lots of species for whom sex is painful, or at least it looks like it must be. Tyson’s responses and @-mentions filled up with biologists and science communicators pointing out spiny penises, traumatic insemination, and other ways that animal mating systems get kinky. A spoof hashtag, #BiologistSpaceFacts, encouraged biologists to turn the tables on Tyson by tweeting (deliberately, hilariously) uninformed descriptions of astronomical phenomena. All of which is to say, it was a pretty fun Friday on Science Twitter.
Then, Saturday, Tyson teed up for another go:


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Posted in evolution, natural history, population genetics, selection | Tagged , , , | 2 Comments

Chromosomal inversion determines male morphs in the ruff

Ruff male of the morph Independent. Photo: Daniel Pettersson Photography

The ruff is a wading bird where the male becomes especially spectacular during mating season with its colorful and variable breeding plumage. Two papers published together in Nature Genetics in November have now identified the genetic source of the large variation of male plumage in a small region of the ruff’s genome.

Males of this species can be divided into three different morphs that both look and behave very different from each other: Independents have colorful plumage with both collar and head tuft. This morph vary greatly in color and they defend their territories violently at leks. Satellites are non-territorial while carrying white ruffs and head tuft. They are slightly smaller than Independents and display submissive behavior. Faeder is a recently discovered, rare morph (Jukema and Piersma 2006), where the males are small, inconspicuous and avoid fighting Independents by mimicking females.

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Coral clonal chimeras

We are all too aware of the threats ecosystem engineers, such as corals, face in light of global climate change.


However, a new study by Rinkevich et al. (2016) suggest chimerism may be a a weapon to combat climate change.
The coral Pocillopora damicornis can release either sexual or asexual planula-larvae. Rinkevich et al. (2016) documented the release of asexual propagules from mosiacked maternal colonies that are chimeras.

In a single clutch, … each of the chimeric larvae presented different combinations of maternal genotypic constituents, altogether creating a unique genetic variability by means of asexual reproduction.

This genetic variability may confer ecological advantages to this type of reproduction. These novel genetic entities have a greater store of variability and may have a much wider range of physiological responses.
Could this be a partial reprieve for some brooding corals?
References
Rinkevich et al. (2016) Venturing in coral larval chimerism: a compact functional domain with fostered genotypic diversity. Scientific Reports 6, 19493.

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A statement on p-values that approaches significance*

Point-oh-five. It’s a pretty polarizing number. Sitting on either side of it could mean the difference between a [insert your favorite journal here] paper and an unpublished paper. But why do some researchers, reviewers, and journal editors put so much weight on this highly influential number? Particularly when it is so often misinterpreted?
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Posted in methods, science publishing | Tagged , , | 3 Comments

Introducing The Fourth Reviewer

(Flickr: Mark Seton)
(Flickr: Mark Seton)

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 now the founder and Managing Editor of Axios Review. Ever since I started at The Molecular Ecologist, Tim had talked about writing an advice column specifically geared toward questions about peer review — and now we’ve finally put it together.

In this column, which we’re calling “The Fourth Reviewer,” Tim will answer readers’ questions about the ins and outs of writing and submitting a paper for review, interpreting editors’ decision letters, responding to reviewers’ comments, and revising for a successful publication. If you have a question for The Fourth Reviewer, send us an e-mail. Questions will be presented pseudonymously, and may be edited for space and grammar — but Tim’s answers will always be his unfettered opinions, informed by years of experience on both sides of the publication process.

Without further ado, here’s our first batch of questions:

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Posted in community, peer review, science publishing, The Fourth Reviewer | 2 Comments

The Evolution of Molecular Dating

Molecular dating is a key tool in deciphering the history of life. In a recent Molecular Biology and Evolution paper, Sudhir Kumar and Blair Hedges have reviewed the state of the subject, summarizing the philosophical and methodological history of this often-integrative endeavor. In particular, their binning of this history into 4 sequential “generations” provides a convenient way of thinking about the evolution of this science, which I paraphrase below.
Generation 1: Assume a strict molecular clock. Utilize all the data.
Generation 2: Don’t assume a strict molecular clock. Utilize only those data that pass tests of clocklike behavior.
Generation 3: Utilize all the data, and allow the molecular clock(s) to vary in rate across phylogeny according to some prior model.
Generation 4: Utilize all the data and estimate relative clock rates but without the need to model rate variation or speciation/extinction.
 
2015-02_clock
 
Generation 3 remains, at present, the dominant paradigm within which many phylogenetic, phylogeographic and epidemiological studies operate. Therefore, Continue reading

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Fred Allendorf receives the 2015 Molecular Ecology Prize

Molecular Ecology's chief editor Loren Rieseberg presents Fred Allendorf with the Molecular Ecology Prize plate. (Fred Allendorf)

Molecular Ecology‘s chief editor Loren Rieseberg presents Fred Allendorf with the Molecular Ecology Prize plate. (Fred Allendorf)


Fred Allendorf literally wrote the book on conservation genetics, as part of a career of research ranging from basic evolutionary biology to studies of the specific genetic risks incurred by rare and endangered species. The 2015 Molecular Ecology prize recognizes these contributions, as Michael K. Schwartz lays out in the award essay in the journal:

Fred was a forerunner in the field of conservation genetics. He has been called the grandfather of the field, in part because he had such an easy grasp of population genetics theory, yet cared about real molecular data and how it could be applied to conserve imperilled populations. In 1986, he published two very important papers. The first called ‘genetic drift and the loss of alleles versus heterozygosity’ (Allendorf 1986), where Fred shows the dangers associated with the use of only heterozygosity to predict the loss of genetic variation during bottlenecks. He notes in this work that the number of alleles that remain postbottleneck will likely be important to the long-term evolutionary response to selection, and thus the survival of a species. … The next important paper was the review of heterozygosity and fitness in natural populations in Michael Soule’s second Conservation Biology book (Allendorf & Leary 1986). Here, Fred was showing how first principles of population genetics should be used to conserve natural populations.

Fred received a silver plate commemorating the prize before presenting in the Biodiversity Research Centre seminar series this week at the University of British Columbia.

Posted in community, conservation, genomics, Molecular Ecology, the journal | Tagged , | 3 Comments

The current people and future content of TME


The crowdfunding campaign to support this blog has reached the first goal: maintaining the basic infrastructure that keeps the lights on. Woohoo!
The next goal? Supporting the people who work hard to bring you interesting content.
Who are we?
We are researchers, postdocs, and PhD students from all around the United States and beyond. In the last two years, the blog has welcomed two cohorts of new contributors that have greatly increased the diversity of perspectives you read here. You may have noticed this as we’ve kicked into high gear over the previous weeks.

 
From local adaptation to population connectivity to phylogenetics. From RNA to ancient DNA. From humans to algae. Someone on the team is thinking about it, writing papers about it, and in the lab working on it.
What do we think you like to read?
Taking a peek behind the curtain of this blog is interesting. Some posts are popular because they provide a basic tutorial for some often-searched technique. Some posts seem to be popular because the right people share it on social media. Some posts are more popular than others for no apparent reason.
However, we do know a couple things for sure.
First, we’ve had many new visitors as we’ve added new contributors:
Created by Jeremy Yoder

Geographic distribution of new visitors to the site in 2015 (by Jeremy Yoder). Special shoutout to that one person in Greenland. We love you.


Second, the most-accessed posts are usually the “long form” posts (>1000 words). Of the top 15 viewed posts of 2015, more than half were long form posts despite this type being many fewer in number than the standard ~500 word post.
So we know you like them. They also take a lot of effort to write.
Supporting the crowdfunding campaign allows the contributors to be paid basic freelance rates to produce the pieces that you like to read the most. 
So what do we have planned?
More financial stability means taking more chances and providing more diversity. We are ready to bring a greater number of “series” to the blog, collections of posts written by individual contributors, teams of writers, or contracted third parties that center around specific themes. Here are some of our pitches:
Research/Career Interviews – Thoughtful interviews with leaders in the field. Interviews from both the past and present of the blog have been well-received and always fascinating. This series would make interviews appear in your feed more consistently.
“How We Work” – I’ve personally been a huge fan of the Lifehacker “How I Work” interviews. Since molecular ecology is a field that is so diverse in field, lab, and computational techniques, we propose that learning more about how people get their work done would be interesting to everyone. What R packages do you use the most? What is your to-do list like? Where do you work best? What makes you most productive?
Molecular Ecology 101 – TME readers love tutorials. But what if you aren’t ready to start tossing out circos plots or Procrustes analyses in R?
We’re proposing a series of “Molecular Ecology 101” posts that would be helpful to readers who are interested more generally in the wide world of molecular techniques. For example, you could search Google for “Tajima’s D” and scour through old papers and wikipedia pages. Alternatively, a TME contributor could combine this information in a single blog post: the history of Tajima’s D, the common uses, some current context for how it is used, and a future perspective.
What else do you want to read? Have a say! Comment below and spread the word so we can make it happen.
 

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Veritas Genetics offers $999 (human) genome sequences

All the chromosomes of a human genome, containing about 3.2 billion DNA bases, which Veritas Genetics proposes to sequence for $999. (Wikimedia Commons: National Human Genome Research Institute)

All the chromosomes of a human genome, containing about 3.2 billion DNA bases, which Veritas Genetics proposes to sequence for $999. (Wikimedia Commons: National Human Genome Research Institute)


Veritas Genetics, a company co-founded by Harvard University geneticist George Church* announced today that it will sequence your genome for less than $1,000. One dollar less, specifically. Up to now, “personal genome” services like 23andMe have used methods that don’t actually read the complete sequence of a person’s genetic code (which is what we usually mean by “genome”), but instead read short snippets of DNA sequence, or even single nucleotide “letters” scattered throughout the genome. Veritas’s myGenome service promises to provide something much closer to 100% of a 3.2-gigabase human genome sequence.
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Posted in association genetics, bioinformatics, genomics, medicine, next generation sequencing | Tagged , , | 3 Comments