Photo by Paul Hebert

It’s a cool species, an important addition to the cadre of species whose genomes have been sequenced, it has a notably large number of genes (>30,000, according to the current annotation — rice has >40,000, by the way), and the lead author of the study was a grad student with me in the same lab. But Daphnia pulex does NOT have a big genome. It’s about 200Mb, slightly larger than Drosophila melanogaster, and about 1/15 the size of the human genome.

1. Misconceptions about evolution.

Check. Here’s a headline from a press release by Rice University: “Sponge shines light on life’s origin”. This is off by about 3 billion years. The subtitle to the press release is also awful: “Genome connects the dots between Amphimedon, animal descendants”. Nope. Amphimedon queenslandica is a modern species and is not the ancestor of any non-sponge animals (and probably not of any sponge species either). The common ancestor of all animals may have been sponge-like, but it was not a modern sponge species.

2. Hype about medical significance.

Check. The original paper itself and various news stories play up the “sponges will teach us lots about how to cure cancer” angle. I’ll be glad when (if?) it becomes unnecessary to tie everything to human health for it to gain support. Sequencing the sponge genome has many merits on its own, but the realities of grant competitions dictate that one must often find a link to cancer or climate change to get funded.

Anyway, kudos to the researchers on an interesting contribution to the animal genome dataset!

UPDATE: Along with Jonathan Eisen, I am glad to endorse the press release by UCSB, which shows how important evolutionary concepts can be weaved effectively into a news report. I *almost* was put off by the use of the term “basal”, which is terribly misleading and some implication that this *species* has been around for 650 million years (it definitely has not), but the story author and the researchers interviewed totally redeem themselves with this: “‘You had some ancestral animal that is long-since extinct, and its descendants became these modern-day sponges that we have, and there were other descendants that became the rest of the animal kingdom –– from jellyfish to baboons,’ said Kosik. ‘We speak of the sponge as being this earliest branching phylum, or group of animals.’ ” I’m not sure who the author of the press release was, but he/she did a very nice job here.

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

Genome 10K Community of Scientists

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

http://www.nature.com/news/2009/091104/full/462021a.html

http://www.ucsc.edu/news_events/text.asp?pid=3333

http://genome10k.soe.ucsc.edu/

A genome may reduce your carbon footprint

This somewhat rhetorical title must excite many scientists, particularly those with ongoing research on biomass, feedstock development, and lignocellulosic breakdown/fermention. With the costs of sequencing rapidly decreasing, and with the infrastructure now developed for almost anyone with access to a computer to cheaply store, access, and analyze sequence information, emphasis will increasingly be placed on ways to apply genome data to real world problems such as reducing dependency on fossil fuel. For the efficient production of bioenergy, this may be accomplished through development of improved feedstocks. This article will consider more closely the impact of very cheap sequence data (approximately 1USD per genome) on improvement of switchgrass (Panicum virgatum L.), a perennial grass well suited to biomass production.

Wow, $1 per genome? That would be sweet!

Click here to watch today’s press conference.

New Tree Of Life Divides All Lower Metazoans From Higher Animals, Molecular Research Confirms

The response:

“It is absurd to talk of one animal being higher than another” (Charles Darwin, 1837)

More information:

Understanding evolutionary trees

(By the way, Rob DeSalle, who is quoted in the story, was one of my postdoc advisors and he definitely understands phylogenies — but the story is pretty sloppy nonetheless)

Generic press release for genome sequencing

Scientists map genome of (insert name).

A team of researchers from (insert university/institute/lockup garage) has completed mapping the genome of (animal/plant/squashy deep-sea thing).

“We were amazed how (strike one) similar/dissimilar it is to the human genome,” said (insert name of lead scientist/grad student/custodian who happened to answer the phone).

The discovery should help scientists (strike all but one) cure cancer/end world hunger/prevent hair loss).

Big hop forward: Scientists map kangaroo’s DNA

Taking a big hop forward in marsupial research, scientists say they have unraveled the DNA of a small kangaroo named Matilda. And they’ve found the Aussie icon has more in common with humans than scientists had thought. The kangaroo last shared a common ancestor with humans 150 million years ago.

“We’ve been surprised at how similar the genomes are,” said Jenny Graves, director of the government-backed research effort. “Great chunks of the genome are virtually identical.”

The scientists also discovered 14 previously unknown genes in the kangaroo and suspect the same ones are also in humans, Graves said.

The animal whose DNA was decoded is a small kangaroo known as a Tammar wallaby and named Matilda. Researchers working with the government-funded Centre of Excellence for Kangaroo Genomics sequenced Matilda’s DNA last year. Last week, they finished putting the pieces of the sequence together to form a genetic map. The group plans to publish the research next year, Graves said.

Scientists have already untangled the DNA of around two dozen mammals, including mice and chimps, which are closer to humans on the evolutionary timeline. But Graves said it’s the kangaroo’s distance from people that make its genetic map helpful in understanding how humans evolved.

By lining up the genomes of different species, scientists can spot genes they never knew existed and figure out what DNA features have stayed the same or changed over time. Elements that have remained the same are usually important, Graves said.

The research is an important step in the understanding of genomes in general, said geneticist Bill Sherman, an associate professor of molecular ecology and conservation biology at the University of New South Wales.

But another genetic researcher was more skeptical of the project’s significance.

“If you are in Australia and you want to show that you are a major player in genomics, then it’s important,” said Penn State University biology and computer science professor Webb Miller. “But two guys in their garage are going to sequence another marsupial very soon.”

Those “two guys” are Miller and Penn State colleague Stephan Schuster, who are working on a shoestring budget to map the genome of the Tasmanian devil, which is in danger of extinction because of a contagious facial tumor disease. Miller and Schuster said their project could lead to a way to keep the species alive.

But check out the last line for the biggest problem in the story.

This isn’t the first time Australia’s unique wildlife has provided evolutionary clues. Earlier this year, scientists mapped the DNA of a platypus and found that it crosses different classifications of animals.

No. They. Did. Not.