Skeptophilia (skep-to-fil-i-a) (n.) - the love of logical thought, skepticism, and thinking critically. Being an exploration of the applications of skeptical thinking to the world at large, with periodic excursions into linguistics, music, politics, cryptozoology, and why people keep seeing the face of Jesus on grilled cheese sandwiches.

Thursday, December 12, 2019

The family tree

One of the things I find endlessly fascinating about evolution is that we can use information we have in the present to infer what happened in the (very) distant past.

And I'm not even talking about fossils, here, as interesting as they are.  As Richard Dawkins points out, even if the entire fossil record ceased to exist, the evidence for evolution would still be overwhelming.  What I'm thinking about is the use of DNA to determine relationships between current species, and from that theorize about when their most recent common ancestor lived, and even what it might have looked like.

This comes up because of a recent paper in Nature that analyzed the genomes of over a thousand different species of plants and algae to construct the most detailed and accurate cladogram (which you can think of as a family tree) of the entire kingdom that has ever been created.  There are an estimated 500,000 species of plants currently in existence, so while this is still using a partial data set, it's pretty damned impressive.

"Some species began to emerge and evolve several hundreds of millions of years ago," said plant physiologist Professor Marcel Quint from the Institute of Agricultural and Nutritional Sciences at Martin Luther University Halle-Wittenberg, in an interview with Science Daily.  "However, today we have the tools to look back and see what happened at that time...   Some of these gene families have duplicated over the course of millions of years.  This process might have been a catalyst for the evolution of plants.  Having significantly more genetic material might unleash new capacities and completely new characteristics."

The results, as you might expect, provided a few surprises.  "We used to think that the greatest genetic expansion had occurred during the transition to flowering plants," said Martin Porsch, also from MLU-Halle-Wittenberg.  "After all, this group contains the majority of existing plant species today.  However, the new data reveal that the genetic foundations for this expansion in biodiversity had been laid much earlier.  The transition from aquatic to terrestrial plants was the starting point for all further genetic developments.  This development was the greatest challenge for plants, and so they needed more genetic innovations than ever before."

"We found an enormous increase in genetic diversity at the time of this transition, after that it reached a plateau," added Ivo Grosse, bioinformatician at MLU-Halle-Wittenberg, who co-authored the paper.  "From this time on, almost all of the genetic material was available to drive evolutionary progress and generate the biodiversity we see today."

So without further ado, here's their cladogram:

It confirmed something that I found fascinating when I first heard about it, back in the early 2000s -- that the division of flowering plants into "monocots" and "dicots" -- familiar to every high school biology student -- needed to be revisited, because "dicot" isn't a monophyletic clade -- all descended from a single ancestor that includes no other descendants.  It was found that the peculiar New Zealand species Amborella was technically a dicot (networked leaf veins, flower parts in fours or fives, two seed leaves) but was far more distantly related to other dicots than monocots (such as grasses, lilies, palms, and so on) were.

Amborella trichopoda [Image licensed under the Creative Commons Scott Zona from USA (original upload author), Amborella trichopoda (3065968016) fragment, CC BY 2.0]

When it was later found that the same was true of water lilies, it clued the geneticists in that there was something seriously amiss with our understanding of the family tree of plants.

So the new cladogram supports the older research, putting Amborella, water lilies, lotuses, and star anise as outgroups within the entire phylum of flowering plants; a self-contained clade with all the monocots next; and the rest of the dicots scattered along the remainder of the tree.

I know I'm a science nerd, and a little over-enthusiastic about genetics sometimes, but I think this research is amazingly cool.  The idea that we could look at a plant's DNA, here in 2019, and infer its relationship with other species from which it branched off hundreds of millions of years ago, is boggling.  It makes me wonder what other surprises are out there in the DNA of the nine-million-odd species of life on Earth -- and also realize that when it comes to understanding the other denizens with which we share the planet, we've only barely begun.


This week's Skeptophilia book of the week is brand new; Brian Clegg's wonderful Dark Matter and Dark Energy: The Hidden 95% of the Universe.  In this book, Clegg outlines "the biggest puzzle science has ever faced" -- the evidence for the substances that provide the majority of the gravitational force holding the nearby universe together, while simultaneously making the universe as a whole fly apart -- and which has (thus far) completely resisted all attempts to ascertain its nature.

Clegg also gives us some of the cutting-edge explanations physicists are now proposing, and the experiments that are being done to test them.  The science is sure to change quickly -- every week we seem to hear about new data providing information on the dark 95% of what's around us -- but if you want the most recently-crafted lens on the subject, this is it.

[Note: if you purchase this book from the image/link below, part of the proceeds goes to support Skeptophilia!]

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