Tuesday, March 10, 2015

Snapshots from research

Pictures from grads while doing research. Sometimes the pictures are directly related to their research, sometimes the pictures are of cool things seen while doing research.


Sharp Shin Hawk by-catch during Gambel’s white-crowned sparrow field collection with mist netting in Eastern Washington. The Sharp Shin became caught while trying to catch a small song bird that had just flown into the mist net. The mist net is visible behind me. -Tracy Larson



A picture of "my office" in both the summer and fall...I study the phenology of those wildflowers! -Elli Theobald



 

On a walk through lion and zebra infested grassland I stumbled upon a bizarre femur in ~255 million year old rock. We found several more like it, but still don't know what it belongs to! -Brandon Peecook


 
I'm interested in the actin cytoskeleton of Giardia. Currently, I'm investigating the biochemical properties of this highly divergent molecule. My previous work focused on localizing the guanine activating proteins (GAP) in Giardia. Blue are the nuclei, red is actin, and green is the putative GAP. -Melissa Steele-Ogus



I spent the last quarter watching leaves grow! -Melissa Lacey


A photo of one of my summer neighbors. I was camping in western Montana for fieldwork. -Jonathan Calede

 
Ever wonder what it looks like when a virus infects bacteria? These charismatic plaques (holes in a bacterial lawn) were created by the bacteriophage Phi 6, which infects the bacterium Pseudomonas syringae which itself infects tomato plants. A pathogen of a pathogen! -Katrina van Raay



Thursday, March 5, 2015

Melissa Steele-Ogus: Immunity and Humanity

Probably the most controversial political issue right now is what should really be a non-issue: vaccination. Hot-button phrases are being thrown around–parental choice, bodily autonomy, personal responsibility. I am deeply troubled by the extremely vocal and fast-growing anti-vaccine (or anti-vax) movement.

This issue affects me personally. I am mildly immunocompromised, and while I do my civic and corporeal duty and routinely get my vaccinations, they aren’t always effective. My body doesn’t reliably react to them in the way it’s supposed to (N.B. this is not a failing of the vaccines themselves, but of my immune system). Additionally, there are others who are more severely immunocompromised and are unable to get vaccinated for medical reasons–most notably, those who have struggled with leukemia, lymphoma, or other cancers. These people rely on herd immunity to keep them safe. This means that those who choose not to get vaccinated are not only putting themselves at risk for preventable diseases, but also risking the lives and health of the immunocompromised population. These people are at a higher risk of catching preventable
This month's National Geographic explores why people doubt science. 
diseases, and are also more likely to suffer lasting, irreversible consequences from it. 


Even though any link between autism and vaccines has been dispelled multiple times, anti-vaxers have been desperately clinging to it as justification to not vaccinate their children. Although misguided, this impulse is understandable. Autistic spectrum disorders are, on the whole, misunderstood, and thus, feared. If people can find a scapegoat for autism, they can hold on to the hope that they can prevent their children from developing it. But this attitude is also incredibly problematic because it devalues the lives and experiences of those with autism. The act of risking the life of one’s child to “protect” them from autism has an unspoken, and terrible meaning: “I would rather my child die than be autistic.”

I can’t deny that I’m worried about my own personal safety, or that the spread of ableist attitude is disconcerting. But what is most distressing to me is the willful ignorance and rejection of technological advancement. As humans, we are incredibly fortunate to control our own destiny. Rational thought is our ecological niche. We have taken hold of our natural abilities and wielded them with such strength that we have eradicated some of the most terrible diseases in our history. We did this, with our own natural talents. To deny these talents, so flagrantly and unyieldingly, at the risk of the health and lives of others of our own kind, is an act that can only be described as inhuman.

When smallpox was eradicated, it was widely considered to be the greatest achievement of humankind. Polio is wiped out in the United States, thanks to vaccination. Before the anti-vaccine trend, measles, mumps, and rubella were on their way to being extinguished as well. We are at risk of losing the gift left to us by our forebears, a gift which belongs to all of us, through a disregard for truth and the safety of others. Shouldn’t we pass this legacy of health, and triumph of the mind, on to the next generation?

Many people are afraid to disturb the seemingly fragile-yet-perfect bodies of their children with foreign substances, like medication. But, vaccines aren't medication. They are technology that utilizes the body's own defenses. The reluctance to inject mysterious substances into the body of one's child is understandable. However, refusing to listen to the advice of pediatricians, immunologists, and other experts and instead placing trust in animal instinct is denying our humanity. It’s giving in to fear. But we aren’t prehistoric primates, huddled in a cave to insulate us from the world. We don’t have to do that anymore.

Wednesday, February 18, 2015

Jared Grummer: Studying hybrid zones between Argentinean lizard species with loads of DNA



At the end of every rainbow is a doctoral dissertation. Photo by Jared Grummer.

I often wonder what non-scientists think of my research: who cares about lizards that they will never see? When I say I study hybrids, do they think I mean hybrid cars? And no, there are no medical applications for my research. Hybridization, or interbreeding between distinct species, of lizards in Argentina is a very foreign idea for most, in more ways than one.

I am a fourth year PhD candidate and I have been interested in hybrid zones for a little while. Hybrid zones offer a unique view into the evolutionary processes that either generate or extinguish species. You see, “species” is a word that the non evolutionary biologist is certainly familiar with, but few know the incendiary debates that regularly occur on campuses worldwide that cover ideas of what defines a species. Just like species, the definition of a species is mutable and evolves over time, largely based on how data are collected. Before Darwin, species have been diagnosed based on morphological (physical/external) characteristics that separate different types of organisms; this lizard is green, and that one is yellow, therefore they are different species. Nowadays, species are mostly being defined based on something all organisms share: DNA.

DNA sequencing technologies that have recently been developed allow us to sequence a large portion of an organism’s genome, therefore shedding light on not only its past, but the past of its ancestors. I still, however, recognize the importance of morphology in determining species limits, those boundaries that separate species. When morphological variation within a “species” is high, it is suspect that more than one species may be present. This point brings us to the lizards!

I am studying a group of lizards in Argentina, the Liolaemus fitzingerii group, that belongs to a lizard genus (Liolaemus) that is confined to South America. This is an exceptional genus of lizards because some species exist at over 5,000m, whereas others are found at sea level; some are herbivorous, and some even give live birth. Furthermore, they are relatively poorly understood and between 10-15 new species are described each year! Regarding the L. fitzingerii group, approximately 15 species are currently recognized, but the geographic and biological boundaries that separate many of these species are not clear.


One of the first male Liolaemus melanops we found during this fieldwork! Photo by Jared Grummer.

I have awesome collaborators, Luciano Avila and Mariana Morando, who are researchers at the National Central Patagonia Institute and they have spent their careers trying to describe the diversity of Liolaemus species and understand their evolutionary history. They have studied the L. fitzingerii group for a number of years, mainly because it is a very difficult group to understand. A lot of morphological variation exists within some species in the group, such as L. melanops, where the males can go from having a completely black head, to no black on the head, and everything in between, in the same locality! This makes determining species solely with morphological data a very difficult task.



The governmental building of my collaborators Luciano Avila and Mariana Morando. Photo by Jared Grummer.
I have come to Argentina during their summer to sample some putative hybrid zones between some of the L. fitzingerii group “species”. We have sampled one area in Chubut province in particular because the extreme morphological variation seen in this species raises this question if this is a single species, or potentially a hybrid zone between two distinct species. Here is some of the variation in this area:



Variation in male dorsal patterning from individuals collected at the same locality. Photo by Jared Grummer.
Variation in male ventral patterning from individuals collected at the same locality. Photo by Jared Grummer.
Sometimes, hybrid zones are found in “ecotones”, where two distinct habitat types come together. However, in this area of Patagonia, the habitat appears to be homogeneous (at least to the human eye).



Liolaemus melanops habitat in Chubut Province. Photo by Jared Grummer.

It is fun to be doing science in an area where Darwin has been! Well, he wasn’t in this exact area, but he was close. In fact, there is a Liolaemus species with his name, L. darwinii, that we have seen a lot during this trip. It was not this species, but Darwin mentions in his notes from the Beagle voyage that he collected a viviparous lizard in Patagonia with a hammer (yikes!).

My collaborator Luciano and I have sampled ~10 sites in northern Chubut and southern Rio Negro provinces spanning an area over 100km that potentially represents a hybrid zone between 2-3 species in the L. fitzingerii group. Now that I have the lizards, the next step will be to collect and analyze DNA from across the genomes of these individuals to see the extent of gene flow between these various populations along a morphological gradient. Half of the vouchers, or physical specimens, will be sent to the Burke Museum of Natural History and Culture; the other half will remain with my collaborators at the National Central Patagonia Institute in Puerto Madryn. These specimens will be a critical reference when analyzing the DNA, as we will be looking for congruence or conflict between morphological and molecular data in this area of putative hybridization between species.

This is my working hypothesis of how hybrid zones have formed. Liolaemus fitzingerii taxa retreated eastward to the historic coastline during Pleistocene glaciation, then expanded westward following glacial retreat and warming temperatures. Species ranges have subsequently come into contact, and hybrid zones are shown in darker grey. Also shown is my hypothesis of genetic diversity as a function of longitude.
I will leave you with some photos of the other cool things that we have been seeing. Stay tuned with results of this research in the spring!


A gecko, Homonota darwinii, that is one of nine Homonota species in Argentina. Photo by Jared Grummer.


A male Liolaemus melanops. Photo by Jared Grummer.


The herpetology lab in CENPAT where we processed all of our samples. Photo by Jared Grummer.


Luciano overlooks a rocky outcrop and ranch in Chubut Province. Photo by Jared Grummer.
Flamingos leaving their laguna. Photo by Jared Grummer.

 A southern sea lion colony during breeding season at Punta Norte on the Valdez Peninsula. Photo by Jared Grummer.



Thursday, February 12, 2015

Biology Graduate Student Retreat 2015

Another year, another grad retreat: hot tubbin', dance/costume party, epic burritos with homemade guacamole thanks to our social committee, hiking, breakfast at the bakery, a trip to the Reptile Zoo, science and grad life talk. We might have the best grads ever.

Unseasonably warm temperatures resulted in little snow this year, so everyone who was planning on going skiing or snowshoeing ended up hiking instead. More BioGrads on the trail ahead! See you next year!


Monday, February 2, 2015

Audrey Ragsac: From Seattle to Brazil

When I walk to work every day, I greet two security guards, walk over a moat, hold my ID card to a sensor that makes the door click open in a satisfyingly sci-fi way, and I walk into the relief of air conditioning from the 90°F plus heat.  I’m in a city of 12 million people, it’s summer in January, and yes, I said a moat.  Needless to say, the experience of walking into the plant systematics lab at the University of Sao Paulo (USP) is quite different from that at UW Biology.

In a way, it feels like I work in a medieval fortress filled with 21st century science. Step inside after crossing the moat, and you will find towering metal cabinets filled with dried plant collections, hear the whir of -80°C freezers, and see labs adorned with the latest in scientific equipment.  The students here say we work “above the waves,” since our building literally sits on top of a small artificial lake.  While it doesn’t make a whole lot of sense for housing the herbarium and labs (moisture and humidity are seen as the enemy in these settings), it’s nonetheless a truly unique and functional place to work. 


Surrounded by water and lush greenery, the plant systematics lab at the University of Sao Paulo is a kind of oasis in the middle of the concrete jungle of Sao Paulo.

Instead of being patrolled by vicious crocodiles, our moat is filled with koi and turtles, and while they provide very little protection against marauders, they prevent mosquitos from breeding and add a little happiness to your day.

I moved to Sao Paulo, Brazil almost exactly three months ago to study the evolutionary relationships of the plant family Bignoniaceae with Lucia Lohmann’s group at USP.  My advisor at UW, Richard Olmstead, has been collaborating with Dr. Lohmann to study this plant group for almost a decade.  The Bignoniaceae is a mainly tropical family containing over 800 species.  Some familiar members of this family, characterized by showy trumpet-shaped flowers, may include North American natives Catalpa, Campsis, Bignonia, and Chilopsis.  The section of the family I’m working on, the tribe Jacarandeae, is limited to the New World tropics and contains about 50 species.  Since I’ve been in Brazil, I’ve had the chance to see these plants in their native range in the northern states of Bahia and Para.


Jacaranda sp. in Bahia, Brazil.

So why on earth would anyone move 7000 miles away from home to study plants when there are perfectly interesting plants in Seattle?  Well, the New World tropics harbor nearly 37% of the world’s plant species, making it the most species rich region on Earth.  Therefore, it is a very exciting place to study the processes and patterns generating plant diversity.  But what are these processes and patterns, and how and in what combinations did they give rise to this incredibly diverse plant assemblage?  Explorers and scientists alike have pondered this question for a very long time.  Through my work on this family of plants, I hope to help answer part of this big question.

In order to do this, the first goal of my work is to generate a phylogeny, or tree-like evolutionary history, of the Jacarandeae using information stored in DNA sequences of each species in the group.  To generate this phylogeny, I am extracting DNA from tissue of each species, amplifying gene regions of interest using a process called polymerase chain reaction (PCR), and then sequencing the resulting amplified DNA.   Once I have sequences from many gene regions, I will feed them into computational statistical programs that use differences between these sequences to determine how the plants they came from are related to one another, ultimately spitting out a phylogenetic tree.  Eventually, I also plan to gather and combine data from both the Olmstead and Lohmann labs to generate a phylogenic tree for the entire Bignoniaceae.  These phylogenetic trees will be incredibly valuable because I can use them as tools to better understand how these plant groups have diversified through space and time across the New World tropics.

Setting up a polymerase chain reaction (PCR) in the USP plant systematics lab.

An additional source of motivation for my work is the high amount of habitat loss occurring in Brazil.  When I had the opportunity to see my plants in the field, I noticed that many locations where my plants had been collected in the not so distant past had been plowed over and built upon.  In Amazonia, there were times when the only landscape you could see were farms and cattle ranches.  Seeing this destruction has given me the drive to work harder to unlock the evolutionary stories held in my plants’ genetic codes before they’re gone for good.
The sun setting over newly cleared land in Amazonia.
In closing, studying these plants isn’t just important in terms of understanding a key phenomenon that has perplexed scientists for eons, but also in terms of cataloging the diversity of threatened ecosystems before they fall victim to habitat destruction.  I hope my remaining three months working above the waves in Sao Paulo will help me to accomplish a little bit of both.

~Audrey

Friday, January 23, 2015

Grad Publications: Dave Slager, C.J. Battey


            As those who attended the Klicka lab talks at last year's GSS might remember, the family Vireonidae encompasses about 52 species of birds distributed throughout the tropical and temperate Americas.  Vireonids are small- to medium-sized arboreal songbirds with a thick and slightly hooked bill.  Many species are omnivorous with a predominantly greenish or yellowish plumage.  The family has traditionally been divided into 4 genera:  Peppershrikes (genus Cyclarhis), Shrike-Vireos (Vireolanius), Vireos (Vireo), and Greenlets (Hylophilus).

With the exception of its starkly colored irides, the White-eyed Vireo (Vireo griseus) is a rather typical vireonid.  It breeds in scrubby forest edge and understory in the eastern United States and northeastern Mexico and winters on the Gulf Coast and Caribbean Islands. © David L. Slager, 6 May 2013, Lucas County, Ohio, USA.

            Until now, the few molecular phylogenetic studies examining the history of Vireonidae have sampled only a small number of taxa, preventing detailed inference about the family's evolutionary history.  By contrast, we were able to sample mitochondrial and nuclear genes from 221 individuals representing 46 of 52 vireonid species, enabling us to break much new ground in understanding the evolutionary history of this important clade.
            Among several key results we (including fellow biograd C.J. Battey!) recently published in Molecular Phylogenetics and Evolution was our finding that the New World Vireonidae is monophyletic group, consistent with a single colonization of the Americas from an Asian ancestor.  We also found preliminary evidence for the existence of several cryptic species in the Neotropics and noted that tropical vireonids contain greater intraspecific genetic diversity on average than their temperate counterparts.  This trend is consistent with data from other bird families, and suggests that regional taxonomic bias or biological processes such as higher tropical speciation rates may be driving the pattern.
            Our phylogeny contradicted the traditional taxonomy of Vireonidae in important ways.  Most notably, we found that the 15 greenlet species in the genus Hylophilus (sensu lato) are not closely related to each other but fall into 4 different clades.  In an attempt to clean up this taxonomic mess, we published a follow-up paper in Zootaxa revising the genus-level taxonomy of the greenlets so that genera reflect monophyletic groups.  We proposed keeping the pale-eyed, scrub-dwelling greenlets in Hylophilus, moving the dark-eyed, canopy-dwelling greenlets to the old genus Pachysylvia, moving Tepui Greenlet to Vireo, and transferring the unique understory-dwelling Tawny-crowned Greenlet into the new genus Tunchiornis.



The canopy-dwelling Rufous-naped Greenlet (Hylophilus semibrunneus) is a core member of mixed-species foraging flocks in subtropical forests of the northern Andes.  Our revised taxonomy places it in the genus Pachysylvia to reflect the fact that it and other canopy-greenlets are only distantly related to the scrub- and understory-dwelling greenlets. © David L. Slager, 7 February 2011, Jericó, Antioquia, Colombia.

            Switching topics away from vireos, a molecular phylogeny of the New World sparrows published in the Klicka lab in early 2014 showed that the American Tree Sparrow (Spizella arborea) is not related to the other species of Spizella sparrows, but rather represents its own lineage with a long, independent evolutionary history.  In our Zootaxa paper, we reviewed the taxonomic and phylogenetic placements of the American Tree Sparrow to date and described a new genus, Spizelloides, for the American Tree Sparrow to allow modern taxonomies to more closely reflect its evolutionary relationships.
            That's all for now.  You'll have to come to GSS this spring to hear what's up next!

--Dave

References

Slager, D.L., Battey, C.J., Bryson, R.W. Jr., Voelker, G. and J. Klicka. 2014. A multilocus phylogeny of a major New World avian radiation: The Vireonidae. Molecular Phylogenetics and Evolution 80:95-104.

Slager, D.L. and J. Klicka. 2014a. A new genus for the American Tree Sparrow (Aves: Passeriformes: Passerellidae). Zootaxa 3821:398-400.

Tuesday, January 20, 2015

Grad Publication: Elli Theobald and Lauren DeBey


Earth is in the middle of one of the largest biodiversity crises in history. Scientists not only have an obligation to document and understand the consequences of this loss, but also address these global changes with new and sustainable solutions. However, this research requires large quantities of data on how the genetic, taxonomic and functional composition of communities is changing over space and time. For example, accurately observing and understanding climate change-induced latitudinal shifts in species distributions may require collecting data across thousands of kilometers. Citizen science has been proposed as a mechanism to gather large volumes of spatio-temporally extensive biodiversity data while simultaneously integrating public outreach into research. Consequently, there has been a proliferation of citizen science programs and similar partnerships between scientists and non-scientists; however, the efficacy of these programs in quantifying biodiversity has not been evaluated.
In our paper “Global Change and Local Solutions: Tapping the unrealized potential of citizen science for biodiversity research” we focus on this critical question facing biodiversity research in the 21st century: can the ballooning global human population be harnessed to effectively contribute to biodiversity research, and specifically to conservation and global change impacts? 

Volunteers counting birds with Christmas Bird Count.


To answer this question we used seven citizen science web-based clearinghouses (together listing more than 500 programs) to create a single database of biodiversity citizen science programs. We considered only programs that focus on biodiversity (defined as documenting the occurrence of taxonomically identified organisms across space and time) and incorporate scientific inquiry (defined as collecting quantifiable information related to a specific issue or question). Thus, in our paper, we provide the first comprehensive and quantitative review of the extent, efficacy, and quality of biodiversity citizen science data. 


Volunteers doing a “BioBlitz” on Cal’s Living Roof Project.
Within the projects we sampled, 1.3 million volunteers participate in biodiversity monitoring, contributing $1.5 billion in-kind annually. We show that the explosive growth in citizen science matches or exceeds scientific interest in biodiversity and global change drivers and shows no signs of declining. Current projects target all vertebrate classes, five major invertebrate phyla, diverse plant families, bacteria, fungi, and even protozoa. We demonstrate that a majority of citizen science projects have a larger spatial extent and higher longevity than most ecological research projects; and that one third have data that are readily available, verifiable, and collected via a standardized, written protocol. Despite these indications of rigor and relevance to biodiversity science, only 12% of projects had Web of Science searchable publications. We conclude that biodiversity science must embrace citizen science as a viable means of data collection, or risk alienating the public that we, as scientists, seek to educate and inform. 

The seven citizen science clearinghouses we searched to create the single database we used in our analysis.
The paper is co-authored by bio-grads Elli. Theobald*, Lauren DeBey, former bio-grad Ailene Ettinger*, and Hillary Burgess, Natalie Footen, Halley Froehlich, Cherie Wagner, Janneke HilleRisLambers, Josh Tewksbury, Melanie Harsch, and Julia Parrish. (*indicates equal contribution)


Check out our whole paper here.