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.

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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!]

Going to the dogs

I am the proud owner of two dogs, both rescues, who are at this point basically members of the family whose contributions to the household consist of barking at the UPS guy, sleeping most of the day, getting hair all over everything, and making sure that we get our money's worth out of the carpet steamer we bought five years ago.

First, there's Lena the Wonder-Hound:

And her comical sidekick, Grendel:

Both of them are sweet and affectionate and spoiled absolutely rotten.  Lena's ancestry is pretty clear -- she's 100% hound, probably mostly Blue-tick Coonhound, Redbone, and Beagle -- but Grendel's a bit of a mystery.  Besides his square face and coloration, other significant features are: (1) a curly tail; (2) a thick undercoat; and (3) a tendency to snore.  This last has made us wonder if he has some Pug or Bulldog in his background somewhere, but that's only speculation.

This all comes up because of a recent delightful study in one of my favorite fields, cladistics.  The idea of cladistics is to create a tree of descent for groups of species based on most recent common ancestry, as discerned from overlap in DNA sequences.  And a group of researchers -- Heidi G. Parker, Dayna L. Dreger, Maud Rimbault, Brian W. Davis, Alexandra B. Mullen, Gretchen Carpintero-Ramirez, and Elaine A. Ostrander of the Comparative Genomics Branch of the National Human Genome Research Institute -- have done this for 161 breeds of dog.

The authors write:

The cladogram of 161 breeds presented here represents the most diverse dataset of domestic dog breeds analyzed to date, displaying 23 well-supported clades of breeds representing breed types that existed before the advent of breed clubs and registries.  While the addition of more rare or niche breeds will produce a denser tree, the results here address many unanswered questions regarding the origins of breeds.  We show that many traits such as herding, coursing, and intimidating size, which are associated with specific canine occupations, have likely been developed more than once in different geographical locales during the history of modern dog.  These data also show that extensive haplotype sharing across clades is a likely indicator of recent admixture that took place in the time since the advent of breed registries, thus leading to the creation of most of the modern breeds.  However, the primary breed types were developed well before this time, indicating selection and segregation of dog populations in the absence of formal breed recognition.  Breed prototypes have been forming through selective pressures since ancient times depending on the job they were most required to perform.  A second round of hybridization and selection has been applied within the last 200 years to create the many unique combinations of traits that modern breeds display.  By combining genetic distance relationships with patterns of haplotype sharing, we can now elucidate the complex makeup of modern dogs breeds and guide the search for genetic variants important to canine breed development, morphology, behavior, and disease.

Which is pretty cool.  What I found most interesting about the cladogram (which you can see for yourself if you go to the link provided above) is that breeds that are often clustered together, and known by the same common name -- such as "terrier" -- aren't necessarily closely related.  This shouldn't be a surprise, of course; all you have to do is look at the relationships between birds called "buntings" or "sparrows" or "tanagers" to realize that common names tell you diddly-squat about actual genetic distance.  But it was still surprising to find that (for example) Bull Terriers and Staffordshire Terriers are more closely related to Bulldogs and Mastiffs than they are to (for example) Scottish Terriers; that Corgis are actually related to Greyhounds; and that Schnauzers, Pugs, Pomeranians, and Schipperkes are all on the same clade.  The outgroup (most distantly related branch) of the entire clade is the peculiar Basenji, a Central African breed with a strange, yodel-like bark, a curly tail, and pointed ears, whose image has been recorded almost unchanged all the way back to the time of the ancient Egyptians.

Anyhow, it's an elegant bit of research, and sure to be of interest to any other dog owners in the studio audience.  Me, I'm wondering where Grendel fits into the cladogram.  Considering his peculiar set of traits, he might have a branch all his own, and give the Basenji a run for its money as the oddest breed out there.