A Desert Tortoise Field Trip

It’s the hottest time of year in the Valley of the Sun, and the unavoidable and unrelenting desert summer heat prevents newcomers such as me and my family from fully exploring our new beautiful surroundings. This is a sad fact, although the reality is that our lives are so upended by the move that we have little room for field trips – it will be better come springtime when (1) we are more settled and (2) daily temperatures will be cooler and the desert will be blooming and full of life. My wife and daughter escaped the heat this week to visit family in Portland, OR – a place with almost opposite climatic conditions from here. The brief northwestern Oregonian summer with its dry warm days and blue blue skies are hard to beat. So I am glad they have a chance to have some fun in the sun without having to worry about their health, like they would here.

Meanwhile, in the Phoenix area I have been relegated to air-conditioned indoor activities at the lab, office and home. Pleasingly, I received an invitation from one of my new colleagues who studies tortoises to join the Arizona Fish and Wildlife Turtle Management Team as a volunteer on a tortoise-monitoring trip. Since I am part of a group that is planning on sequencing the Desert Tortoise genome for its conservation, I thought it was a serendipitous opportunity to actually meet one of our possible study organisms. We were to meet the team at the Sugarloaf Mountain Area in the Tonto National Forest, about one hour northeast of downtown Phoenix. In the summer, these excursion need to start early – both humans and animals need to avoid the midday heat – so I picked my colleague up at 4:30am. The habitat was beautiful. It’s amazing that these sprawling desert landscapes contain large desert reptiles!

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The Sugarloaf Mountain area in Tonto National Forest. There are tortoises wandering around this landscape, and we were searching for both tagged and un-tagged individuals.

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Here comes one now!

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Close-up of a desert tortoise (Gopherus morafkai)

The team did manage to find tortoises but I forget the exact number. I was much more of a spectator on this trip, as it was my first excursion into the desert since we moved our here, and my field search image is not attuned to tortoises. So while these photos are my own, I had to rely on other more experienced folks to actually find the animals. They really just look like desert rocks, and they freeze when they see a person.

The extremely competent members of the turtle team were taking vital measurements of each tortoise as part of a long-term study tracking the growth and movements of desert tortoises that live in this part of the Sonoran Desert.ImageBeing out in the desert afforded an opportunity to see other reptiles, of course. Here are some pictures of an earless lizard (genus Holbrookia). During one rest point for the team, this individual was perched on a nearby rock giving us the business – which in lizard language consists of nasty looks and push-ups.Image

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You think you can take me?

Out of all the reptiles, you have to admire the chutzpah of some lizards. Upon being approached by humans, tortoises hide in their shells, snakes slither silently away, alligators dash messily to the water’s safety… but many species of lizards give humans displays of dominance almost right up until the last minute. Then they run away of course. But for the first few seconds it always seems like the little lizards really are sizing you up and thinking they can take you on.

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Believe it or not, the tortoises love this rocky terrain!

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I Moved My Family Across the Country for a Postdoc

It sounds weird to make this confession, as if it represents a wrong act that no one should commit. Even before we got married, my wife and I agreed on the fact that we both wanted to move out West, and once we did tie the knot we remained certain that it was the cardinal direction for us to have the kind of life we wanted. We would have more space, more freedom of movement, most likely in a house rather than a one bedroom apartment, with a driveway to unload groceries without risking either our lives being double-parked or a ticket while at the fire hydrant. I would be done with grad school, and my wife could put her exhausting job behind her, and we could focus on the future and put our daughter into bed each night after tasting the orange bliss of western sunsets (sound of clinking Chardonnay glasses here).

I am exuberantly excited to begin work at Arizona State University, gain experience as a senior person in a productive lab and learn a whole new set of analytical tools that will make me a better scientist. Still, as most things in life, there is a complicated duality here. I’m native New Yorker who was born and raised in Queens, lived in Brooklyn, educated at NYU and CUNY, and almost all of my friends and relatives would remain on the East Coast. Other than my new colleagues and a few cousins (with a big Italian family like mine, there are always a few relatives in some state somewhere), we know barely anybody here. How will we fit into a state whose politics we basically abhor? The reality of this major life change is that it is very difficult to move a family across the country for a postdoc, and it is wrought with opportunity but also doubt, hardship, and confusion. In fact, the title of this post is derived from Google searches I have made in search of help.

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Velma on the flight to Phoenix. Is it too late to change our minds?

Through the Eyes of Our Cat

You probably can appreciate how difficult it is to put your whole family on a one-way trip with all your possessions either packed with you or on a moving truck somewhere else. If you haven’t done it, you’ve certainly marveled with horror watching other people do it in airports. So I will skip to the funniest part of the trip which would have to be the little side story of our obese cat, Tiny.
I have to start Tiny’s story with the fact that we acquired a prescription for Xanax to keep him calm during the plane ride. A vet wrote him up for eight 0.25mg pills, which is a human-sized dose. We tested him a week before for we left for any side effects, which means we currently still have six doses of kitty Xanax which may or may not come in handy someday.
The helpful folks at airport security told me I had to take Tiny out of his travel bag and carry him through the metal detector with me. There was huge collective gasp from all the other travelers when they gazed upon the one we lovingly refer to as Big Tuna. He was obviously mortified as we waited for the pink (yes, pink) bag to come through the X-ray machine, with him sitting upright on my lap like a giant fat furry angry buddha.

At that moment Velma decided to do a little of her patented kitty torture – comprised of horrible acts that cats hate, like cuddling and hugging and kissing, which of course made things even worse for Tiny. He made it clear he would rather be locked up in the bag and jumped right back in it and stayed there without a peep for the next 7 hours.

When we landed in Phoenix, we put a doggie harness on him and brought him to the “pet relief” area – really a dog run – with hopes that he would urinate and drink some water. He was too petrified to do either of those things, especially when the dreaded shihtzus began to show up. Anyway, he is doing fine now and enjoying the desert shade underneath our backyard oleanders so I think it will be a happy ending for Tiny.

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Enjoying some well-deserved patio time.

Other items of import:

Our Parents Have Been Living with Us Since We Moved

We love our parents. We would be nowhere without their support. So I am just going to skip this section and move on.

Our Daughter has Adopted Strange New Sleep Habits

By the time we were getting ready to leave NY, Velma had become a champion sleeper. Not every night was a breeze, but we all went to sleep fairly sure that she would be down for about 11-13 hours a night. This was after a typically rough first year of her life. Now it is all up in the air again, whatever gains were made in the sleep department have been lost. She falls asleep in her bed, but by 3am every night she has silently slipped into our room and joined us. At about 4:30am she starts to spin and kick. Imagine if someone yanked a large fish out of the sea, put it in toddler pajamas, and tossed it into bed with you. It would make a good punishment for a misdemeanor (“I hereby sentence you to one year in bed with kicking two year old”).

More anecdotes another time…

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Welcome to your new home…


You’re a Doctor Now

Last week marked my official joining of the ranks, my gaining of the heralded admission ticket to a career in academic research. I was extremely proud to receive my Ph.D. diploma at the 49th CUNY Graduate Center Commencement Ceremony, which was held at Avery Fisher Hall in New York’s Lincoln Center. I had defended my Ph.D. almost two months earlier, and much of the lingering fatigue from the arduous process of thesis-writing had worn off. Having since moved on to other more collaborative research projects and already securing a postdoctoral research position at another institution, I thought the fact that I had deposited that old dissertation  – literally leaving the hulking paper mass composed of my own blood, sweat and tears on a desk in the CUNY library – had meant that I was already done with it all. Yet even a cynic such as myself could not deny the ceremonial importance of donning a cap and gown, lining up in front of faculty, administration and  families; having a robe placed over my head signifying my entry into the intellectual elite. I gotta admit: it felt kind of good. My only wish was that I could bring the people who have helped me during this process, such as family and friends and especially my wife, onto the stage to wear some well-earned robes of their own. I couldn’t have done this without them.

I thoroughly credit the CUNY institution for giving me the opportunity to earn a Ph.D. in Biology, although I must admit that it wasn’t always easy being a CUNY student. I have met many academic colleagues (other grad students, post-docs and P.I.s) in my field, exchanged ideas, and sometimes competing with them. Some came from programs and institutions that were undeniably better funded  than mine, and to a certain degree more focused on fostering cultures of excellence (although not necessarily accessibility, which I have always applauded CUNY for). These places seemed to us to coddle their students like priceless dragon eggs (and isn’t that what all us poor grad students really want?). In contrast, CUNY students can easily get lost navigating the labrynthal bureaucracy and general lack of funds in the public higher education system, often relying on time-consuming teaching assignments that, while rewarding, may ultimately sap their abilities to produce published research – the true test of academic success in science. But that’s just me complaining: I have always believed in the CUNY mission and May 23rd, 2013 was a glorious day, for about 450 CUNY doctoral students proved that they now can, and really always have been able to, play with the big boys.

The commencement address was given by David Nasaw, the Arthur M. Schlesinger, Jr. Professor of History at the CUNY Grad Center. Since the early 1970s, Nasaw has written books on a wide a range of topics from how to start a high school to a biography of Joseph Kennedy.  In his speech to us, he talked about the illusion of historical objectivity in scholarly pursuits. Using the metaphor of a river, he described how  knowledge flows through time, getting passed down from generation to generation, and our struggles to interpret it along the way. As it is impossible to remove those who observe the universe from the universe itself, our current dogmas may eventually with time appear more temporary and fleeting than absolute.

I wonder which steadfast approaches in my of own fields in molecular evolution and population genetics will become obsolete and seem naive and subjective to their own time. Indeed, the structure of evolutionary theory has wavered along a spectrum ranging from adaptationist views of natural selection being the dominant force of evolutionary change and another where neutralist views explaining mutation and genetic drift are more favored. The quickening pace of advance in genomic sequencing technology will no doubt bring about newly observed patterns, perspectives, and theories about the process of biological evolution over the next decades. Through all the ups and downs, CUNY has given me the tools to be a part of the next paradigm shift.


Breaking Up (Anolis) Is Hard to Do

The “Anolisphere” is all abuzz with a recent paper by Nicholson et al. published in the journal Zootaxa with the inviting title, “It is Time for a New Classification of Anoles”. The authors propose two important and potentially disruptive changes to some widely-accepted features of the study of Anolis lizards:

1) The currently recognized genus Anolis is actually comprised of eight ancient lineages that are so divergent it is justified to break Anolis into eight genera (DactyloaDeiroptyx, Chamaelinorops, AnolisXiphosurus, Ctenonotus, Audantia, and Norops).

2) The widely accepted “ecomorph” hypothesis, which states that several independent lineages of Anolis lizards underwent convergent adaptive radiations on Caribbean islands (I wrote about this in a previous post), is not supported by the evidence.  The authors therefore suggest a looser-fitting “ecomode”model, which simply describes similar ecological adaptations without having to invoke any deterministic process.

The phylogenetic tree from the Anolis genome paper (Alfoldi et al. 2011). Nicholson et al. (2012) suggest that the eight lineages on this tree are so divergent they merit separate generic status.

Jonathan Losos of Harvard University has referred to this paper as “undoubtedly the most important paper on anoles to be published in the last several years”. Nonetheless, these intriguing ideas will require long and heated debate before they are to be accepted by the scientific community as a whole.  The editors of the anole-themed blog Anole Annals have already staked out a position as being strongly opposed to the changes. It has already been suggested that the Anolis community need not be compelled to formally adopt the new classification, and that it would be disruptive and confusing for future researchers, given the long body of work in which Anolis is referred to as a single large genus. There are also mounted defenses of the new paper as well. Check out what’s happening on the blog this week.

In my opinion, we should keep the single-genus status of Anolis, and here’s why. Pretty much everyone in evolutionary biology agrees that Linnean classifications (the binomial system which assigns genus and species names, as well as higher order classifications such as family, class, phylum, etc.) should reflect the monophyly of groups. This means that if you are describing a new genus, or family, or class, the number of lineages nested within the new group is largely subjective and the only real criterion is that all the lineages have descended from a common ancestor.

When basing taxonomy on the estimation of phylogenetic trees (which is pretty much how it’s done these days since tree building is how one establishes monophyly), your taxonomies are only going to be as good as the trees you use. Granted, the tree in the Nicholson et al. paper has strong statistical support, but that only really means that it does a good job of describing the data used to construct it in the first place. If down the line there is more or better data, a new tree may have better support, and then new taxonomies will have to be proposed. Since our understanding of taxonomy is dependent on phylogenetic information that is subject to change, and since we can say with certainty that Anolis in the broad sense represents a monphyletic group, AND much of the research out there treats it as such, I think we’re better off just keeping Anolis the way it is. But up to this point, I’m a consumer of systematics and not an authority on this by any means.

You’re staying put, honey! Whatever happens, Anolis carolinensis will remain in the genus Anolis.

The question remains, can a single genus be ~130 million years old? And the answer is absolutely yes. While our genus, Homo, is only just over 2 million years old, Ginkgo is probably about 200 million years old. And they’re both considered genera! My point is that Linnean classification, while useful, really serves a purpose in the sense that someone knows what museum drawer to put these things in. And I think Anolis should be one drawer (with almost 400 species, that’s a big drawer!).

In any case, under the newly proposed taxonomy, the species I study, A. carolinensis, will remain in Anolis. So I have little to lose, other than a divorce from hundreds of other fascinating possibly former congeners.


Rejection Pretty Much Sucks

I recently learned I won’t be offered a postdoc I really wanted. There are other pending and as yet unrealized opportunities. Rejection is always a risk in science (papers, fellowships, grants, and now jobs), and everybody gets a lot of it. I knew these things going into the postdoc job market.

But sometimes when you come so close to something you can almost taste it, and you start to imagine yourself living in that not-yet-happened situation, working in that very lab with those very people, moving your family to the region – what neighborhood would we move to? Where are the nearest daycares? Oh, it’s so much better than Brooklyn, because we can afford a backyard… Reality can really smack you right in the face, and it’s a huge letdown.

But it’s not over. Other opportunities abound. I have skills, publications, and darn it, people like me!

I’ll get back up. I am still filled with resolve. The future is going to happen, anyway, right? Sigh…. Sometimes, resolve is so much work, you kind of want to just sleep in and drink a little coffee while reading The New Yorker for a while. Reminds me of these guys:

I am the battle-worn king inspiring my army, which is also me (and my wife and child) into the battle of our lives – THE FUTURE!!! Which will be sometime in the morning, just after some odds and ends we have to do, and maybe a little me time, perhaps?


The Story of Our Green Anole Story, Part 1

Our paper on green anole phylolgeography has been published, so I thought I would justify the study in the first place and briefly synopsize our major findings and their implications. There’s a lot to talk about, so it will be completed across two posts.

First, some background….

As you may know, Anolis carolinensis is the scientific name for the green anole, which is a smallish lizard that lives in the southeastern United States. Last year, its complete genome sequence was published. At the time, it was the only reptile to have a fully sequenced genome (although this list is ever growing) and the phylogenetic gap it filled among sequenced vertebrates created a real demand. In addition,  Anolis carolinensis is the lone species — out of a genus of around 400 — which occurs naturally in North America, with the bulk of Anolis biodiversity situated in South America and the islands of the Caribbean. On these islands, several independent yet convergent adaptive radiations led to the evolution of the same “ecomorphs” on different islands (a nice blog-post-sized review can be found on this Map of Life page). It’s a lovely story.

Separate adaptive radiations on separate islands led to the repeated evolution of Anolis ecomorphs, which is one of the most elegant stories in evolutionary biology. The genome will unlock the genetic secrets of this phenomenon. Image from Lizards in an Evolutionary Tree by J. Losos, and adapted from the work of E. WIlliams.

What does the Anolis genome offer? The chance to understand the genetic basis of adaptation (discussed by the eminent evolutionary biologist Jonathan Losos in this blog post on the Anole Annals), which is a very exciting prospect indeed. Using the genome as a resource, biologists may be able to pinpoint exactly which parts of the genome are affected by natural selection as new species form, or as different populations adapt to new surroundings. On another note, our lab wanted to look at how natural selection shapes the structure of a genome by limiting the activity of transposable elements, and the Anolis genome offered a unique opportunity to address this important question in comparative genomics. With regard to A. carolinensis specifically, it lives in a wide variety of habitats from subtropical Florida (FL) to more temperate Tennessee (TN), where anoles are subjected to freezing winters. The genome opens considerable opportunities for investigators to learn the genetic basis of each population’s unique set of adaptations across this landscape.

There was one problem, and it is familiar to anyone who studies population genetics (an esoteric bunch, indeed, however this is a major field in biology): if you want to know how much of the genetic variation in a population is affected by natural selection, you have to first have an estimate of the total amount of expected genetic variation (a parameter known as θ, or Theta). One thing that significantly affects θ is population size (usually denoted as N; the other thing affecting θ is the mutation rate u, so that θ=4Nu): a large population will have more genetic variation. But in order to measure the size of the population, you need to know its structure. What does that mean? Well, in a wide-ranging species (like A. carolinensis), it is very unlikely that individuals living in, say North Carolina are able to mate and share genes with those from Texas. Through a process called genetic drift (which is the random changing of gene frequencies due to finite numbers), these separated populations will resemble each other less and less over time. Understanding structure allows biologists to measure the amount of gene flow across landscapes, which can significantly alter local population sizes. Once you have an idea of the population structure, only then can you estimate the population size and measure natural selection at the genetic level.

In addition to estimating population sizes, looking at how genetic variation is distributed geographically allows researchers to make inferences about the evolutionary history of a species. For instance, if you were to observe that certain fixed genetic differences occur on either side of a large river, it may be due to the fact that the river provides a dispersal barrier. If you know how old the river is, you may be able to estimate how long the populations have been separated. Applying these methods to the understanding of the history and formation of species is a field in biology known as phylogeography. Phylogeography had its origins in the late 1970s, and as it became more practical to study genetic variation (especially after the advent of PCR and DNA sequencing), it exploded in the 1990s and 2000s, and now has at least one technical journal (aptly titled Molecular Ecology) solely dedicated to publishing studies using its methods. The phylogeography of a species is of special importance with regard to θ, because if the history of the population includes exponential growth (as it would when a receding glacier reveals virgin habitat) it will skew the θ estimates downward.

Pretty much what was known about Anolis carolinensis after the invention of PCR and DNA sequencing. Map modified from http://www.terrariet.dk/Anolis_carolinensis_UDB_UK.html

What was known about the phylogeography of green anoles? Well, not much. It was established that A. carolinensis arrived from Cuba sometime near the Pliocene-Pleistocene boundary about ~3 million years ago — an “Out of Cuba” hypothesis. The last study that looked at genetic variation in the species was Wade and Echternacht (1983), which relied on the differential electrophoretic movements of proteins called allozymes from anoles collected at seven localities. The major findings were: (1) 17 out of 25 allozymes completely lacked variation and (2) South FL was the home of the most divergent anole population. I like this paper, but it didn’t delve deep enough to make any robust inferences about green anole evolutionary history. This is nothing against the authors, it’s just that the methodology and technology weren’t strong enough yet.

English: Green anole (Anolis carolinensis) (ma...

Hey, phylogeographers! Study me!

Since then, as major advancements were made in the application of robust evolutionary models to more easily attainable DNA sequences for phylogeographic inference, the green anole escaped the scrutiny of phylogeographers, even as more and more co-distributed taxa were looked upon. It seems as if this widespread, abundant and even iconic lizard had become completely overlooked. It wasn’t as if samples were hard to come by. In fact, if you were to search HerpNet for museum samples of green anoles, you would receive 9,548 records! We had done our own fieldwork as well, and several questions were left wide open for us to address: (1) what is the structure of green anole populations across its range and just how divergent are the major lineages; (2) are the often-cited common dispersal barriers associated with co-distributed taxa also correlated with the distribution of genetic variation in green anoles; and (3) how did the glacial history during the most recent ice ages effect green anoles living at higher latitudes? So we decided to give it a try.

I’ll talk about the paper in Part 2.


Academia Less Attractive to Senior Grad Students

A very interesting study published in PLoS ONE turned up in my RSS feed this week. It looks at how graduate students in the sciences change their outlooks on careers in academia as they progress. PhD students in the life sciences, chemistry, and physics were asked to rate the attractiveness of various careers. The researchers wanted to see if the answers given depended on how long the student had been in grad school. The results, especially for the life sciences, were striking. The later the stage of program progress for the student, the less likely he or she was going to find a faculty-teaching or faculty-research position as “extremely attractive”. In all fields, careers in “other” or “startup firm” become much more attractive to grad students as they near graduation.

Students rated careers as “extremely attractive” by field and stage in program. From Sauermann and Roach (2012).

Two other things to take home from the results of this study that the authors point to: (1) it is right to be concerned that there are far fewer tenure track faculty positions in academia than the market of graduating students will demand, and (2) the fact that PhD advisors strongly encourage academic career paths to their students reflects a growing disconnect with what actually may be attainable.