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

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Aerosteon riocoloradensis: a new dinosaur from Argentina

Flesh rendering of the predator Aerosteon with the body wall removed to show a reconstruction of the lungs (red) and air sacs (other colors) as they might have been in life.

Flesh rendering of the predator Aerosteon with the body wall removed to show a reconstruction of the lungs (red) and air sacs (other colors) as they might have been in life.

Greg Laden has the scoop on the new Argentine dinosaur that was featured on Daily Planet. It is called Aerosteon riocoloradensis.

Fossils of a newly discovered species of dinosaur — a 10-meter-long, elephant-weight predator — were discovered in 1996 along the banks of Argentina’s Rio Colorado, and are now being reported after a long period of careful study. This dinosaur dates to about 85 million years (which falls within the Cretaceous period).

Perhaps the most interesting feature of Aerosteon riocoloradensis is that it demonstrates the evolution of a bird-like respiratory system in an animal that is definitely not bird-like in most other ways. Indeed, the authors of this paper imply that this dinosaur’s respiratory system represents an early phase in the evolution of the bird’s respiratory system. This is a case of an adaptation arising in one context and later being used in an entirely different context.

Aerosteon riocoloradensis also represents a previously unknown group of South American dinosaurs, which may be ancestral to allosaurs.

Bora Zivkovic at A Blog Around the Clock also has an article: a new dinosaur with hollow bones.

I always get excited when Paul Sereno publishes a paper in PLoS ONE and today is one such day – his third paper in this journal within a span of less than a year (the first was the paper with detailed description of Nigersaurus and the second was the article on Green Sahara cemeteries). Today’s paper is also the second time PLoS ONE publishes a taxonomy paper, i.e., a monograph that describes a new species:

Evidence for Avian Intrathoracic Air Sacs in a New Predatory Dinosaur from Argentina:

Paul Serano, you’ll remember, is National Geographic’s Explorer in Residence.

Blog monkey needs your help

Dr. Marc van Roosmalen is trying to protect this new species of black, woolly monkey and other new species in the Amazon jungle.

Cutest monkey ever

Cutest monkey ever

Donations will help to fund his research and protect the habitat for these animals. If he gets $31,000, he promises to name it the Blog Monkey — Lagothrix blogii.

Hat tip to PZ Myers at Pharyngula: “Blog Monkey.”

Strange fish may belong to new family

An unusual fish from Indonesia. could be part of a new family. It’s an anglerfish but does not have a dangling lure. Instead, it has a flat face and keeps close to coral reefs, where it uses its stiffened pectoral fins to burrow into crevices, looking for something to eat. Only anglerfish, apparently, have crooked, leg-like pectoral fins. University of Washington Professor Ted Pietsch, a leading authority on anglerfish, has never seen anything like it. DNA analysis will be done on the fish to determine whether it constitutes a new family of bony fish.

a new kind of anglerfish

The fish was discovered in January, 2008.

Ten weirdest, coolest new species

MSNBC’s science section highlights ten new species discovered last year that are the weirdest, coolest, or most venomous.

Styloctenium mindorensis, a newly discovered fruit bat from Mindoro

Platypus genome, the paper

swimming platypus by Peter Arnold

Nature 453, 175-183 (8 May 2008) | doi:10.1038/nature06936; Received 14 September 2007; Accepted 25 March 2008.

We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

Books: The Whole Hog by Lyall Watson

cover, The Whole Hog by Lyall WatsonI just finished reading this most enjoyable book, The Whole Hog by Lyall Watson, all about superfamily Suoidea: pigs (family Suidae) and peccaries (family Dicotylidae), but not hippos.

The book describes the domestication, species, and subspecies of pigs, the story of pigs and explorers, and the sensorium and intelligence of pigs. Watson is right: pigs are inexplicably overlooked when we think about domesication, culture, and animal intelligence. Except as stand-ins for humans in medical research, they are little studied.

Watson makes a good case for them more-or-less domesticating themselves, as they are sociable omnivores. Signs of pig domestication have been found at least 8,000 years ago. But do we hear about that great advance, the domestication of the pig? We do not. We hear about dogs, cattle, horses, and cats. He describes his childhood pet, a fostered baby warthog, that accompanied him and his guardian on walks through the African bush.

There’s a tiny population of Himalayan pigs which average about ten pounds—perhaps a better pet than the 80-pound Vietnamese pot-bellied pig. They are unique—and threatened—but is anyone their champion? He tells of the discovery of a remnant population of Giant Peccaries in Yucatan in the 1970s. Until those were discovered, we believed that they had gone extinct 10,000 years ago.

Find a copy if you can.

Superfamily Suoidea. comprises two familes.

Family Suidae:

  • Subfamily: Suinae – “true” pigs
    • Genus: Sus (pigs)
      • Sus scrofa (domestic pig) – many subspecies
    • Genus: Potamochoerus (river hogs)
      • P. larvatus, bushpig
      • P. porcus, Red River hog
    • Genus: Hylochoerus (forest hogs)
      • H. meinertzhageni – forest hog, four subspecies
  • Subfamily: Phacochoerinae – warthogs
    • Genus: Phacochoerus
      • P. aethiopicus, desert warthog
      • P. africanus, common warthog
    • Subfamily: Babirousinae – babirusa
      • Genus: Babyrousa
          • B. babyrussa
          • Family: Dicotylidae
            • Genus: Tayassu (peccaries)
            • Genus: Catagonus (giant peccaries)
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