Categories
Bottlenecks

Coalescence at bottlenecks

This is Part 1 of my response to Dr Dennis Venema’s second Biologos Blog “Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 2)”. Dr Venema was responding to my blog at Nature Ecology and Evolution Community about his book Adam and the Genome. Since Dr Venema’s Part 1 blog responding to me, a vigorous debate has been ongoing on the Biologos Forum here. This debate is now beginning to come to a conclusion, so I have a bit of time to respond to the Part 2 blog by Dennis, which branched out from the Forum debate. Here is Part 1 of my response.

Categories
News

Babbage Podcast (The Economist) interview on tree health

Just before Christmas, I was interviewed by Howie Shannon for The Economist’s “Babbage” podcast. Here it is!

Categories
Bottlenecks

Response to Dennis Venema’s Blog “Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1)”

This is my response to Dennis Venema’s Biologos blog that he posted after I published my email and blog at Nature Ecology and Evolution Community about his book Adam and the Genome. This text is also placed as a comment under Dr Venema’s blog post on the Biologos blog page.

Dear Dennis,

I am glad that we are now establishing a dialogue about the scientific credibility of a bottleneck of two at some point in the history of the human lineage. I am hoping that during the course of this discussion we will be able to examine in detail the claims that you make in chapter three of Adam and the Genome, and that you will respond to all the critiques and questions that I have raised in my email to you and my blog at Nature Ecology and Evolution Community.

Categories
Bottlenecks Genomics

Responding to Felsenstein, Schaffner and Harshman at The Skeptical Zone

Here is the text of a comment I posted at The Skeptical Zone in response to comments by Joe Felsenstein, Steve Schaffner and John Harshman on my Nature Ecology and Evolution blog on human bottlenecks:

Thank you all for interacting with my Nature Ecology and Evolution Community blog, and thanks to Vincent Torley for posting here. Vincent kindly sent me a personal email pointing out this thread to me and asking me to specifically interact with comments made by Steve Schaffner and Joe Felsenstein. I will also comment on John Harshman’s comments as he is making the strongest case against a bottleneck of two, which was not mentioned explicitly by Dennis Venema in his book chapter.

Categories
News

Marcus Wallenberg Prize 2017

This blog was first posted at Nature Ecology & Evolution Community on 31 October 2017

Last week in Stockholm the forest geneticist Prof. Ron Sederoff was awarded the Marcus Wallenberg Prize. Informally known as the “Nobel Prize for Forestry”, this two million Swedish Krona award is presented by the King of Sweden each year. It is the first time for a decade that the prize has gone to a biologist.

In the 1980s, Ron Sederoff realised that molecular genetics had the potential to transform research on trees.

Categories
Bottlenecks Genomics

Adam and Eve: a tested hypothesis?

This blog was written for the Nature Ecology and Evolution Community where it is posted here.

Comments on a recent book chapter

Does genomic evidence make it scientifically impossible that the human lineage could have ever passed through a population bottleneck of just two individuals? This is a question I am asked semi-frequently by religious friends. With my current understanding of the genetic evidence, I can’t state categorically that it’s impossible. In this view, I find I differ from a recent book chapter on the topic. I’m writing this blog to run my thoughts past other biologists, and check I am not missing something.

Categories
Bottlenecks

Email to Dennis Venema about human population bottlenecks

A few months ago, I was reading a new book by Dennis Venema and Scot McKnight entitled Adam and the Genome. I was surprised to find a claim within the book that the past effective population size of humans has definitely never dropped below 10,000 individuals and that this is a fact of comparable scientific certainty to heliocentrism. I emailed Dennis Venema, the biologist author of the book, to query this. Unfortunately, he has not yet responded. I therefore remain unconvinced that it is a scientific impossibility for human beings to have all descended from a single couple. If I am wrong, though, I would like to know. I therefore post my email here, in hopes of garnering responses to my objections.

Categories
Genomics Research

“Abundant bioactivity” of random DNA sequences?

This blog was written for the Nature Ecology and Evolution Community where it is posted here.

Probing the claims of a recent study

Readers of this blog will be aware of the recent Nature Ecology and Evolution paper entitled “Random sequences are an abundant source of bioactive RNAs or peptides”. Rafik Neme, the first author, posted an engaging Behind the Paper blog here.

On a quick look, I thought the study might be the beginnings of the solution to the mystery of orphan genes. (I posted about orphan genes here a few months ago.) The paper appears to demonstrate that an unexpectedly high percentage of random 150 base-pair DNA sequences are functional when expressed in E. coli. If true, this would suggest that de novo gene evolution could occur easily from junk DNA.

Categories
News Research

Darwin’s abominable mystery

This blog was written for the Nature Ecology and Evolution Community where it is posted here

One of the hidden gems of Royal Botanic Gardens Kew is its library. I spent several happy hours there researching a recent letter to Nature Ecology and Evolution, published in June under the title “The deepening of Darwin’s abominable mystery“.

Categories
Ash Genomics Research

The evolutionary mystery of orphan genes

This blog was written for the Nature Ecology and Evolution Community where it is posted here.

Every newly sequenced genome contains genes with no traceable evolutionary descent – the ash genome was no exception

This week in Nature I and my co-authors published the ash tree genome. Within it we found 38,852 protein-coding genes. Of these one quarter (9,604) were unique to ash. On the basis of our research so far, I cannot suggest shared evolutionary ancestry for these genes with those in ten other plants we compared ash to: coffee, grape, loblolly pine, monkey flower, poplar, tomato, Amborella, Arabidopsis, barrel medic, and bladderwort. This is despite the fact that monkey flower and bladderwort are in the same taxonomic order (Lamiales) as ash.