Monocots Evolved from Aquatic Plants says Molecular Study

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I'm not a plant expert, but I can tell monocots from dicots.

Apparently the monocot lineage was founded by aquatic plants (Science mag news story, original paper) and some obscure monocot leaf structure features can be explained by that aquatic origin.

I'm actually kind of surprised something like this has not been done before.
I would have thought that, based on their value in agriculture, this would already have been done to gain a better understanding of their organisms.
Perhaps its just an improvement of things done previously I had never heard of.

This is another phylogenetic study where relationships are being better resolved by the vastly greater number of character traits that can be tracked by using markers provided in some way by molecular genetics to resolve relationships where the limited number and traditional anatomical, biochemical, and physiological traits are uninformative (too few traits spread too far to sufficiently resolve differences).

An example of this can be found in fish phylogenies. Traditional fish phylogenetic studies might use a few hundred anatomical (or other kinds of) traits to determine how to categorize the relationships among many different fish species.
Modern molecular studies produce many more traits to score across these species differences. Each nucleotide base in a sequence of billions of bases can be a trait (although most will get ruled out as being "un-informative"). There will still be large numbers of traits. One study (like in this freely available zebrafish study) uses ~20,000 different, non-repetitive, mapped rad sites that can be analyzed among about 20 species.
It is now even possible to compare fully sequenced genomes containing a few billion bases of primary sequence information. Danio (the genus in which zebrafish are found) has experienced a lot of research on their phylogenetics. Zebrafishers appreciate the usefulness of phylogenetic information and phylogeneticists like being able to relate thier findings to a fully sequenced and annoted genome. There are also, now, a lot of fully sequenced species among the fish related to zebrafish. Researchers are passing around whole genome sequences on thumbdrives.
More independently score-able markers will generally give a more strongly supported and more detailed phylogeny.

Traits previously used to define phylogenetic relationships (anatomical or other traits) will become traits that are mapped onto the new phylogenetic tree, to gain a better understanding of their own evolutionary history as well as the evolution of the species in which they reside.
This is happening with the plants like other well studied organisms.
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Molecular phylogeny is far from new. The first work on it was done by GHF Nuttall in 1904, comparing species' blood proteins by finding cross-species immune reactions. He would inoculate rabbits with blood for various species to provoke immune reactions, and he'd then see which other species' bloods the rabbit's blood would react with (Blood immunity and blood relationship; a demonstration of certain blood-relationships amongst animals by means of the precipitin test for blood : Nuttall, George Henry Falkiner, 1862-1937 : Free Download, Borrow, and Streaming : Internet Archive).

But that work got started in a major way when it became feasible to sequence proteins in the 1960's. Chimpanzee ones turned out to be so similar to their corresponding human ones that some researchers joked that the differences between the two species were mostly cultural (The Bullfrog Affair). Around 1970, biologist Carl Woese recognized that molecule comparisons could be useful for resolving how bacteria are related. He started work on small-subunit ribosomal RNA because that is universal among cellular organisms. He snipped those RNA's up with an enzyme and then compared the collections of fragments. He found that eukaryotes like yeast formed a well-defined group, and that bacteria did also. But one day, he sequenced a methanogen, and bang! It was about as far from other bacteria as eukaryotes were. He sequenced some more, and that methanogen was far from alone. He thus discovered a major split in the prokaryotes, between Eubacteria / Bacteria and Archaebacteria / Archaea. He thought that eukaryotes were a coequal branch of cellular life, but later work points to eukaryotes being a hybrid of Archaea and Bacteria, with the informational systems deriving from Archaea and the metabolic systems largely coming from Bacteria.

Among eukaryotes, protein and gene sequencing supported about 2/3 of Lynn Margulis's revival of the endosymbiotic theory of eukaryotic organelles. Mitochondria are descended from alpha-proteobacteria, and chloroplasts from cyanobacteria, formerly blue-green algae. The remaining 1/3, flagella and cilia and similar parts, are unlikely to be derived from other organisms. The eukaryote flagellum, with its characteristic 9+2 structure of microtubules, is likely ancestral, and its origin continues to be obscure, but it is not some symbiotic bacterium.

The first molecular eukaryote family tree showed animals, plants, and fungi together, with microsporidia and Giardia branching off much earlier. This turned out to be an artifact called long-branch attraction, and starting in the late 1990's, a new eukaryotic family tree emerged, one that has been overall stable for the last 20 years. Choanoflagellates are the closest one-celled organisms to animals, as one would expect, and this group, Holozoa, is the closest group to the fungi proper, with both being Opisthokonta. The oomycetes ("egg fungi") turned out to be in Stramenopiles, closer to diatoms and kelp than other fungi. Opisthokonta and Amoebozoa (most amoebas) turn out to be their closest relatives, as Amorphea. The others are a more motley collection. Alveolata contains the malaria bug, dinoflagellates, and ciliates, and Rhizaria some shelled protists called foraminifera and radiolarians. There also some testate or shelled amoebas. Microsporidia turn out to be a one-celled fungus, like yeasts, and Giardia a member of Excavata, including Euglena. Then there are a lot of one-celled eukaryotes that are difficult to place.
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In the animal kingdom, most species are in Bilateria, the bilaterally-symmetric animals, and their main split appears in molecular-evolution results: Protostomia vs. Deuterostomia. But beyond that, it gets different. Among deuterostomes, hemichordates are closest to echinoderms instead of to chordates, and protostomes are split into the Ecdysozoa and the Lophotrochozoa. The Ecdysozoa, the molting animals, have a subgrouping called Panarthropoda, and also nematodes and some very obscure worms. Lophotrochozoa or Spiralia includes mollusks, annelids, brachiopods, bryozoans, and flatworms. The annelids, best-known for earthworms and leeches, have a surprising member: the tube worms of hydrothermal vents.

Panarthropoda includes arthropods, onychophorans (velvet worms), and tardigrades. Among the arthropods, insects are an offshoot of the crustaceans. Spiders and other arachnids are not classified as true insects, and their insectlike features are from convergence -- loss of most of their legs and gills.

Turning to plants, molecular-phylogeny work has caused a major reorganization of the angiospherms or flowering plants (Magnoliophyta). Older systems made the dicots and the monocots coequal groups, but recent work splits the dicots into eudicots (most of them) and a motley assortment of early branchers. Both eudicots and monocots branched from within those early branchers' branching. Eudicots are distinguished from other dicots by having tricolpate (three-grooved) pollen.

However, molecular phylogeny has not been as successful with the seed plants. They are traditionally divided as gymnosperms and angiosperms, though angiosperms might descend from some gymnosperm. I'll split gymnosperms up here:
  • Angiosperms
  • Ginkgo biloba
  • Cycads
  • Conifers
  • Gnetophytes: Gnetum spp., Ephedra spp., and Welwitschia mirabilis (a very weird plant)
Gnetophytes have been especially controversial, with older studies placing them closest to the angiosperms, and recent ones closest to the conifers ("gnetifer") or even to Pinaceae ("gne-pine").
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Molecular phylogeny is far from new
Very nice post with a lot of well researched information.

Mitochondria are descended from alpha-proteobacteria
New research actually suggests that mitochondria may descend from a yet to be defined group of bacteria outside of alpha-proteobacteria:

However, molecular phylogeny has not been as successful with the seed plants.
Any hypotheses as to why that may be? Have scientists just not sampled enough species to construct a robust phylogenetic tree or does some genetic process in seed plants make phylogenetic reconstruction difficult?
  • #5
(On resolving the seed plants)
Have scientists just not sampled enough species to construct a robust phylogenetic tree or does some genetic process in seed plants make phylogenetic reconstruction difficult?
Rapid divergence can make it difficult, and similar difficulties have appeared elsewhere. Molecular phylogeny has yielded a phylogeny of the placental mammals that goes roughly like this:
  • Boreoeutheria
    • Euarchontoglires: Euarchonta (primates and relatives), Glires (rodents, lagomorphs)
    • Laurasiatheria: Eulipotyphla (various insectivores), bats, Cetartiodactyla (even-toed ungulates and cetaceans), Perissodactyla (odd-told ungulates), pangolins, carnivores
  • Xenarthra: armadillos, sloths, anteaters
  • Afrotheria: various insectivores, Paenungulata (hyrax, manatees, elephants)
Of these groups only Xenarthra has support from phenotypic features, like extra joints in their vertebrae. The rest are almost all from molecular work with some biogeographic support: Boreoeutheria is largely North American and Eurasian, Xenarthra mostly South American and Afrotheria largely African. However, it has been difficult to proceed further, and I've seen:
  • Atlantogenata: Xenarthra, Afrotheria
  • Epitheria: Boreoeutheria, Afrotheria
  • Exafroplacentalia: Boreoeutheria, Xenarthra
A list that covers all the possible branching orders of those three. They could have diverged too fast to be resolvable.
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Another case of rapid divergence is in birds. Resolving them has been surprisingly difficult. Their orders are well-resolved, but the orders' relationships are not. This is from a lot of older work:
  • Palaeognathae: ostrich, emu, cassowary, kiwi, rhea, tinamou, and the recently extinct Aepyornis and moa
  • Neognathae:
    • Galloanserae: Galliformes (landfowl: chicken, pheasant, turkey, quail, ...), Anseriformes (waterfowl: duck, goose, swan, ...)
    • Neoaves (all the rest)
The first divergence is distinguished by details of jaw anatomy, while the second one is from a lot of the older molecular work. But Neoaves has been intractable until recently: Whole-genome analyses resolve early branches in the tree of life of modern birds Needing whole genomes ought to be a good indicator of how difficult it has been. They find:
  • Passerea:
    • Telluraves:
      • Australaves: falcons, parrots, Passeriformes (includes most songbirds)
      • Afroaves: hawks, eagles, owls, New World vultures, woodpeckers, ...
    • Aequornithes: lots of waterbirds: pelicans, gulls, penguins, ...
    • Various other birds, like hummingbirds and cuckoos
  • Columbea: has landbirds like pigeons and waterbirds like flamingos
These are rather motley mixtures and some traits have rather scattered distributions, like liking water and vocal learning.

The authors suspect that an effect called "incomplete lineage sorting" is responsible for the discrepancies between the individual phylogenies that they found. This is for when different gene variants drop out in different populations, thus giving the genes different histories.
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I'll now return to seed plants.

I've found yet another version of gnetophytes and conifers: the gnecup hypothesis, making gnetophytes closest to Cupressaceae, the cypress family. Cupressaceae = cypress, juniper, redwood; Pinaceae = pine, fir, spruce. Thus giving:

gnetifer, gnepine, gnecup

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes | BMC Evolutionary Biology | Full Text The authors used 78 genes, though some of them were absent from some sequences. This gave a total of 58,347 base pairs (bp). They then constructed trees using their original data and also some modifications of it:
  • ntAll: their original data
  • ntNo3rd: with only the first two nucleotides in a codon, since the third one is much less constrained than the first two
  • RY: purine vs. pyrimidine (adenine, guanine vs. thymine/uracil, cytosine), because mutations between purine (2-ring) and pyrimidine (1-ring) are less common than mutations in those categories.
  • AA: codons translated into amino acids. Gets what's selected by a protein's function.
They watched out for "GC bias", because genomes vary widely in their fractions of guanine and cytosine (G+C) as opposed to adenine and thymine, and that can push close G+C organisms together and far G+C organisms apart. It also biases which amino acids proteins may have, High G+C tends to make amino acids with GC-rich codons, while low G+C tends to make amino acids with GC-poor codons.

With all that methodology out of the way, I'll mention its results. Viridiplantae ("green plants") includes land plants and green algae. It has a split between Chlorophyta (most green algae) and Streptophyta (some green algae, with land plants). In the latter, land plants branch off from among the algae, and this analysis has consistent results for land plants' closest alga relatives. About non-seed plants, it is fairly consistent with some discrepancies.

For seed plants, it made all present-day gymnosperms (Acrogymnospermae) sister to the angiosperms, meaning that the ancestral seed plant branched (ancestor of the angiosperms, ancestor of all present-day gymnosperms). For the gymnosperms, it found

( (cycads, ginkgo) (Pinaceae, (Gnetophyta, Cupressaceae and other conifers) ) )

Thus supporting a sort of gnecup+ hypothesis.
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Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes with two nuclear genes, LFY and NRY, finding

(cycads, (ginkgo, (Pinaceae, (Gnetophyta, Cupressaceae and other conifers) ) )

gnecup+ again

Phylotranscriptomic analysis of the origin and early diversification of land plants | PNAS -- uses lots of ranscriptome data. That's working from messenger RNA's, here from nuclear genes. It had two phylogenetic-tree illustrations, and in both of them, gymnosperms were monophyletic. Their trees:
( (cycads, ginkgo), ( (Gnetophyta, Pinaceae), other conifers) )
( (cycads, ginkgo), (Gnetophyta, conifers) )

Thus supporting gnetifer and gnepine.

The authors suspect an early rapid divergence in gymnosperms, one that makes it difficult to sort out conifers and gnetophytes.
  • #9
From molecular-evolution research, it's been possible to find evidence of whole genome duplications (WGD's) or polyploidy events.

Early genome duplications in conifers and other seed plants | Science Advances -- finds evidence of genome duplications in ancestral seed plants, an ancestor of Pinaceae, an ancestor of Cupressaceae and some relatives, and an ancestor of Welwitschia. Didn't try to resolve conifers and gnetophytes, however.

The timing of whole genome duplication | Proceedings of the Royal Society of London B: Biological Sciences -- discusses evidence of a WGD in seed-plant ancestors and one in angiosperm ancestors. The seed-plant event: 399–381 Ma (mid-Devonian), The angiosperm event: 319–297 Ma (late Carboniferous (Pennsylvanian)).

Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data | Genome Biology and Evolution | Oxford Academic
Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms: Molecular Plant
From the latter one's abstract:
The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approximately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes.
That gene loss is what happens after a WGD -- some members of the resulting gene pairs drop out. However, both of them could be retained while being selected in different directions.

What Is the Role of Genome Duplication in the Evolution of Complexity and Diversity? | Molecular Biology and Evolution | Oxford Academic -- notes three WGD events: one in ancestral vertebrates, one in ancestral gnathostomes (jawed vertebrates), and one in ancestral teleost fish (most present-day fish species).

Jawed-vertebrate hemoglobin is two copies of two chains (alpha, beta) arranged in a square with each diagonal having the same kind of chain. The two chains are the result of some early-vertebrate genome duplication. Vertebrate Hox genes are some more genome-duplication heritage, with rather patchy survival.

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