Tuesday, February 16, 2016

Saturday, November 7, 2015

Tortoise Splitters II

Totally for real this time.
This here article, facebook'd to me by Chris Clarke, is pretty cool. Marshalling new and old genetic evidence, they show convincingly that the Galapagos island of Santa Cruz (aka Indefatigable) hosts not one but two genetically and geographically distinct populations of tortoises. This means one species (or subspecies, depending purely on opinion) (Chelonoidis porteri is the species version) gets Officially Split, with the newly identified Eastern population dubbed Chelonoidis donfausti (or C. nigra donfausti).
'kipedia link

The coolest part of the article to me, though, was their Fig. 2, showing a phylogenetic tree for all specimens of Galapagos tortoises that have been sequenced to date, including lots of museum specimens:

Which, ignore the nighbor-joining expercise on the right and check out the beeyootiful tree on the left there. Clades marked in red and orange are the two populaitons from Santa Cruz, and you can see how different they are in context.
As I sez to Chris on Facebook I sez "why no map of the islands with that tree mapped on there?" I sez and then I sez "Now I have to do it myself" I sez and then "also shell shapes oughta be mapped on that tree there too" sez I.
So here's my map [click to N-large]:
Where the amoebas enclose nested genetic clades according to the tree. Island by island, there have evidently never been tortoises on Genovesa and Marchena, hence the Xs. Tortoises are extinct on Floreana, Santa Fe, Pinta, and absent-and-maybe-extinct-but-maybe-never-really-there on Rabida (small) and Fernandina (new), hence the slashes.

Here's a simplified version of the big detailed tree, showing populations by island with color coding corresponding to the map [clickable]:
 ...where X marks extinct taxa and the circled S, I, and D tags refer to Saddle, Intermediate, and Dome-shaped carapaces, as per the Intro from the article at hand here.
For reference, slightly different lists of recognized species (or subspecies) are  here ('kipedia text and photos, here (text), and here (map) [differ mainly in recognizing or not the populations on the 4 other volcanoes of Isabela].

And so but if we naively and foolishly but heuristically take the genetic data at face value, then the tree plus map means that:
1. There are two main groups of GTs; one (1) comprises populations from Santiago and Volcano Wolf, the northernmost volcano of Isabela (where the new pink iguana species was found not long ago...uh...  link), and the second (2) is everybody else (green lines on map). That split represents a very early dispersal event. The northwestern Wolf/Santiago clade is in relatively new territory, but seem to represent an ancient lineage. (Galapagos tortoises probably evolved on islands that are long gone to the southeast).
2. Clade 2 separates nicely into two clades corresponding to eastern (2E) and western (2W) areas. The convincing thing about the article at hand is that the two populations on Santa Cruz belong to separate branches of this split. The newly named species (or subspecies) is marked with a star.
2A. Dome-shaped carapaces look to have evolved separately in the two Santa Cruz species (or subspecies). That, or saddle shapes evolved at least 6 times independently. Maybe a nice example of eviolutionary convergence.
3. Within the eastern clade 2E, samples referred to Santa Fe are most distinct. That's interesting because Santa Fe's purported population is listed in the references linked above as "disputed" and "of doubtful existence," apparently deriving from but a few bone fragmen ts. But if the DNA is that different, one's doubt dissapates a bit. The green coding of the speciment numbers in Fig. 2 of the article at hand means data from museum specimens that were previously reported; I have not dug back to find where.
4. Pinta island tortoises were most closely related to the once-relict-but-now-a-thriving-conservation-success-story torts from Espanola, way the hell down at the totally other end of the archipelago. [the last Pinta Island tortoise, the well-known Lonesome George, is specimen # abiLG in the tree. I have photos of him alive in 2009 someplace.]
5. Over in the western clade 2W, tortoises from the little island of Pinzon are most distinct. One of the 'kipedia articles linked above sez that there is yet a third distinct tortoise population on Santa Cruz, in the northwest, and that they are closest to Pinzon animals, which would be cool.
6. The disputed population from tiny Rabida looks like a transplanted Isabela tortoise, and the specimens attributed to the various volcano-based species (or subspecies) of Isabela are all pretty well jumbled together in this analysis. Maybe should be lumped back into C. vicina as on the linked map.
7. The "doubtful" population from Fernandina is interesting. It's from a single specimen (1906) and no other evidence of tortoises has ever been found there. Here it looks genetically distinct, but closest to the tortoises from southwest Santa Cruz. Except that the Santa Cruz animals are dome-shaped and the speciment allegedly from Fernandina is said to be saddled. And Santa Cruz is clear over on the other side of Isabela and Pinzon from Fernandina. WTF.

All in all, some satisfylingly tidy stories of vicariance, and some puzzles too. It's complicated.

Tuesday, July 8, 2014

hello world

1 tall glass, ice
Frank's Hot Sauce, too much
shot of Evan Williams bourbon
top off with last 2/3 can of Rolling Rock, now warmish

Enjoy alone.

Hello, World.

Monday, March 25, 2013

I'd rather see centipedes


...than not see whatever they're eating.

Sunday, January 27, 2013

Tony Soprano out of context

Cunnilingus and psychiatry brought us to this. season 1 ep 13

Saturday, June 16, 2012

Tuesday, May 1, 2012

cast of Enterprise 2

Cdr. Charles "Trip" Tucker III is a chimera-character. I'm prety sure he's designed to combine the homespun Southern charm, best-personal-friend-o-the-cap'n role, and emotional-homunculus-on-the-right-shoulder trope-purpose of McCoy with the more cynically targeted appeal-to-young-women function of Chekov*, wrapped up in Scotty's old crew-slot.

Unfortunately he comes across to me mostly like a Pensacola frat-boy. Since I already know he gets the girl woman Vulcaness in the end, that's kind of a drag.

* even to me, tuning in to the second-season primetime premier the night before my 8th birthday, it was clear that Chekov was a Russian Davy Jones.

Friday, April 27, 2012

Heart of Cheney

I just learned that Dick Cheney received a heart transplant a few weeks ago.
They say he had suffered "at least five" heart attacks, the first at 37 yoa. Many of us have always suspected, however, that his real cardiac problems were similar to The Grinch's:
3, maybe 4 sizes too small?
In any case, the guy's heart was so dead that for almost 2 years he was a cyborg, with an implanted pump doing the work that his left ventricle couldn't. No pulse.
here's the device:
I forget where I got this pic; maybe the NY Times.
Now it's all been pulled out and he walks yet among the living with somebody else's heart.
But it's the end of a beautiful metaphor.

On the cast of Enterprise

Hoshi is the nerd's Mary Ann to T'Pol's nerd's Ginger.

UPDATE 4/30/2012: bwa-ha!!! 2004!

Saturday, April 21, 2012

100 Outstanding US Journalists. and years.

Here's the list.

All the usual suspects you'd usually suspect, but I smiled to see many of my favorites:

John McPhee!
Garry Trudeau
Rachel Carson
Howard Cosell (yes, I'll stand by that)
Tom Wolfe

The rest (the Professor + Mary Ann), with nice bios for everybody at the link above.

Sunday, April 1, 2012

an old poem

Ring around the rosie,
 a pocketful of posie.


We all fall down.

Sunday, March 18, 2012

classic Star Trek dialog

Absoluely  critical moment:
Season 2, Ep. 1: Amok Time @ ~20.00:
Kirk [of Spock, to McCoy; and defying direct Starfleet orders]: I owe him my life a dozen times over: Isn't that worth a career?!
He's my friend.

Monday, October 31, 2011

Sunday, August 21, 2011

People for the Ethical Treatment of Opisthokonts

...or Deuterostomes, or Lophotrochozoans, or whatever.

[the point being, y'see, the completely arbitrary whim by which "animals" is typically defined]

Thursday, July 14, 2011

not my chair

yeah, I just saw this for the first time the other day. Sue me.

Wednesday, June 29, 2011

You read it here first

...unless you, you know, didn't.

Idea for a new social media platform: combine Blogger and Twitter.
People can issue 'bleats'.

as they follow the flock, see...

Tuesday, June 28, 2011

Tortoise splitters

According to Bob Murphy et al. the desert tortoise ought to be split into at least two species, called Gopherus agassizi (California/Nevada/Utah) and G. morafkai (Arizona and, for now, Sonora and Sinaloa).

My reaction to most taxonomy papers is basically The Dude's:

But as opinions go, I guess Bob Murphy's is a good one.

I am happy they used the opportunity to coin a new North American tortoise name to honor Dave Morafka; he was a good guy.

Look for serious conservation/political fallout from this one.


here's a FAQ

and here's a map:

Friday, May 6, 2011

nother Hero

because at the moment  I am digging Reese and the Smooth Ones (1969), Lester Bowie:

Wednesday, April 6, 2011

there goes the East Mojave

UPDATE: oh dear. Google Earth has updated to the post-landrape landscape.
Well, rest assured that both photos now (4/21/2012) show early stages of the planned landrape construction and so pretty soon, I guess, with further updates at G**gle's end, the contrast will go the opposite way.
damn it.

Ivanpah Valley, north of I-15.
Then, via Google Earth:

View Larger Map

Now, via Basin and Range Watch

Thursday, March 24, 2011

Wednesday, March 23, 2011

Wednesday, March 16, 2011

Saturday, March 5, 2011

re: the Thread, anymore

I will stipulate the almost incredibly passive-aggresive nature of this post.
have a nice day

Sunday, February 27, 2011

Two years of the as yet interminable Thread

So that's two years, 175.76 subThreads, 135,539 comments.
Year Two alone accounted for 144.76 of the subThreads and 107,490 of the comments (= 79%).
Here's the overview:
Fig. 1: [click to enlarge] Comment count for the first two years of Pharyngula's Endless Thread. The colorful vertical lines mark each of the first 50 or so subThreads, but I gave up on that shit. Red threadmarkers with adherent vestigial green threads mark anastomoses. The pink threadmarkers are the 1- and 2-year marks. Somewhere in there in light blue are the parallel subsubThreads CXXVb and CLXIIb.

Up, up up. It's a long way from last year for damn sure.

Thursday, February 10, 2011

by pretty much unpopular request

man, am I loath to re-enter this conversation, but

Wednesday, January 26, 2011

Wednesday, December 8, 2010

posted in memory of someone I did not know

for SC
Hemiphractus fasciatus via Jerry Coyne

Kermit the Frog via Jim Henson

Monday, September 20, 2010

The Colors of Christmas Through the Decades

White Christmas (1942)

Green Christmas (1958)

Blue Xmas (1962)

Black Christmas (1974)

Yellow Christmas (1986)

(Charlie) Brown Christmas* (1992)

Orange Christmas Orange (2003)

*yeah, kind of a stretch. *shrug*

Thursday, August 26, 2010

last chance? please help

Laura Cunningham photo.

If enough people write letters in the next few days, it seems there is a chance to stop the TopKill of a big chunk of Ivanpah Valley.
Please read and act if you can:
Save Ivanpah Valley

Wednesday, August 11, 2010

depressing news

I used to know this place really well*.
Read it and weep.
I did.

*I spent a good part of three years just below the first 'e' of 'Preserve' in the map shown here. Keep reading.

Saturday, July 24, 2010

teh Truth

Biology is always more complex than you think.

Friday, July 23, 2010

bivalves vs. amniotes

This post at Tet Zoo reminded me of a photo I had stashed away. Apologies for utterly forgetting the source.

This is a juvenile stinkpot (Sternotherus odoratus) killed by a freshwater mussel of some sort.

Nature! Red in tooth uh valve and um claw umbo.