New phylogeny research for seed-bearing plants

A massive analysis of 23,000 sets of genes representing most genera of plants has produced what the New York Times calls a makeover for the tree of life. They used the genomes from 150 plants but used supercomputers to identify groups of genes to compare. The seed-bearing plants go back 300 million years, to cycads and conifers, which are gymnosperms–plants with naked seeds unprotected by tough coatings. Those with protected seeds are called angiosperms.

The computer flagged certain proteins as having special significance for the functioning of plants, which could be the keys to important evolutionary relationships. Of the hundreds identified, the scientists randomly selected a few for testing, which confirmed their hunch that those proteins were responsible for plants’ following different evolutionary roads. Some of these relationships date back 300 million years, when the first gymnosperms, the group that includes pines and ginkgos, appeared.

Among other things, they’ve solved the position of gnetophytes.

The scientists organized the results into a phylogenomic tree according to their evolutionary interrelatedness, which included some surprising insights. For example, gnetophytes, a group that consists of shrubs and woody vines, are the most primitive nonflowering seed plants, according to the researchers’ analysis. Those plants date back to the Mesozoic “age of the dinosaurs” and form the base of the evolutionary tree of seed plants.

Here is one of the phylogenetic trees that resulted from this massive re-analysis:

Seed-bearing plants

Quick reference: phylogenies

Carnivore phylogeny:

Family tree of carnivores, dividing into dog/bear and cat branches, then smaller branches

Carnivore family tree

This is the kind of basic information that everyone should know.

Some of the words on this link go to sub-trees, but most of them go to pictures of example animals.

Other trees:

  • Phylogeny of the mammals. Four major branches of mammals are defined:
    • Afrotheria: a diverse group of mammals originating in Africa
    • Xenarthra: a group once included in the order Edentata (anteaters, armadillos and sloths).
    • Euarchontoglires: a group that includes the Primates and the Glires (Rabbits + Rodents) as sister taxa.
    • Laurasiatheria: includes the Ungulate orders (Perissodactyla and Artiodactyla), Carnivores, Pangolins, Bats and Insectivores.

Physiology of the unglates:

Ungulate family tree divides the odd-toed from the even-toed plus whales

Ungulate family tree

Note that the closest living relative of whales are hippos! Since the discovery of transitional fossils linking whales to the hoofed animals, orders Artiodactyla and Cetacea have been combined into Cetartiodactyla.

Also check out

Trees like these were originally devised to trace similar characteristics between species and to systematically group them into more or less similar. Only later was it realized that these trees also represent bonds of common ancestry.

What’s a herptile?

Due perhaps to some Victorian notions about progress, warm-blooded animals were considered “higher” and more advanced than cold-blooded ones, which were grouped together on the low end of the phyogenetic tree. Thus birds (of mysterious origin) and mammals (coming from mammal-like reptiles) were considered close. The study of everything cold-blooded but with a skeleton (coming from fish, not an arthropod or mollusc) was herpetology. The organisms thus lumped together are called “herps” for short. But gradually we realized that turtles, snakes & lizards, and frogs aren’t really very similar.

PZ Myers on Pharyngula supplied the diagram that contrasts our traditional divisions of culturally “similar” animals with their real descent. He also throws in a cartoon about herpetologists.

Birds are descended from active, predatory, warm-blooded dinosaurs, which are descended from early reptiles, as are crocodiles, turtles, and lizards & snakes. Reptiles and their descendents except for birds is a paraphyletic group because it excludes some descendents of the common ancestor. Reptiles and all their descendents is a proper monophyletic group. Lizards & snakes, Frogs, and turtles are a polyphyletic group, because they exclude groups that are closer to the included groups than those groups are to each other. Birds plus mammals is also polyphyletic.

I thought mammals came from mammal-like reptiles, but we now know that mammals and reptiles are sister groups with a common ancestor. (See Amniota.)

Simplified tree of life

From Wikipedia Commons and the Wikipedia article on Evolution, here’s a highly simplifed “tree of life.”

Green dinosaur: Hydatellaceae

Hydatellaceae, an obscure family of dwarf, aquatic flowering plants. is a survivor from before the evolutionary split between dicot and monocot plants. (A monocot has one leaf in the seed, like grass, and a dicot has two, like a bean.)

Previously, the Hydatellaceae were thought to be in the Poales (the order of flowering plants including grasses, sedges, bromeliads, etc.). Instead, they are early angiosperm plant family that belongs near the very root of the evolutionary tree of flowering plants. (The flowering plants began to diversify at least 135 million years ago, in the age of the dinosaurs.)

Through DNA analysis and morphological investigations, the researchers found evidence that the Hydatellaceae are more closely related to the Nymphaeaceae, or water lilies.

The research team was led by scientists at the UBC Botanical Garden & Centre for Plant Research. The researchers, led by UBC Associate Professor Sean Graham and his graduate students Jeffery M. Saarela (now at the Canadian Museum of Nature) and Hardeep Rai.

The discovery was announced in the March 15, 2007 issue of Nature. As noted in the abstract to the article, this discovery rewrites our understanding of angiosperm structural and reproductive biology, physiology, ecology and taxonomy”.

Fly phylogeny

These three scientists

  • David K. Yeates, CSIRO Entomology PO Box 1700 Canberra AUSTRALIA
  • Rudolf Meier, Department of Biological Sciences, National University of Singapore, SINGAPORE
  • Brian Wiegmann, Department of Entomology, North Carolina State University, Raleigh NC USA

Have published FLYTREE, an online phylogeny of the true flies. Their introduction states:

The insect order Diptera (true flies) is one of the most species rich, anatomically varied and ecologically innovative groups of organisms, making up around 12% of the known animal species. An estimated 125,000 species of Diptera have been described, however, the total number of extant fly species is many times greater. The living dipteran species have been classified into about 10,000 genera, 150 families, 22-32 superfamilies, 8-10 infraorders and 2 suborders (Yeates & Wiegmann, 1999). The monophyly of Diptera is well established. Hennig (1973) lists 37 autapomorphies some of which form morphologically complex structures such as the specialized mouthparts adapted for sponging liquids.

They also have pictures, species highlights, morphology, terminology, and useful links to sites such as Diptera.

Book: The Velvet Claw

This special book tells the story of the carnivore family: cats, dogs, weasels, bears, and their kin. In a classic evolutionary pattern, the family tree has branched and been pruned, branched and been pruned, over millions of years. It is based on a BBC television show and has many illustrations.

I highly recommend this book for anyone who is interested in natural history, loves animals, wants to understand evolution better, or wants to get to know the Carnivore family. It explains what a carnivore is and introduces us to the few animals descended from the earlier members of the family, such as the Swift Fox. There is a precis of The Velvet Claw at Bob

New phylum for funny little worm

This worm is so different from everyone else we know that it merits its own phylum. Just to be clear, molluscs are a phylum, chordates (which includes vertebrates as a sub-phylum) are a phylum, sponges are a phylum… it’s a major division based on body plan. This body plan is Blob. Click here for a list of the other phyla. If I remember correctly, science hasn’t discovered a new phylum for at least 10 or 15 years, since a new one was found living on the lips of a larger fish.

P. Z. Myers at Pharyngula says:

A rather thorough molecular study of the organism has accumulated sufficient sequence information to place it in a phylogenetic tree, and it falls into the deuterostome clade, along with us chordates, echinoderms, and hemichordates. At the same time, it’s different enough that the investigators believe it warrants its very own phylum, the Xenoturbellida, bringing the number of extant deuterostome phyla up to four.

For more, read his article about Xenoturbellida

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