Two Ph.D. student positions available at UCB and SDSU

Students will be team members in an NSF-funded multidisciplinary research project: The Genetic Basis, Biosynthetic Pathways and Evolution of Geadephagan Chemical Defense that includes collaborations among researchers at UC, Berkeley; San Diego State University; University of Arizona; and Steven’s Institute of Technology.

The Will Lab, ESPM Department and Essig Museum of Entomology, University of California, Berkeley, is seeking a graduate student interested in working on understanding the function and evolution of defensive chemistry in Adephagan beetles with a preference for students with a master’s degree and a background or strong interest in insect chemical ecology, molecular biology and phylogenetics. This student could start as soon as fall 2016 if he/she makes the 1 Dec 2015 application deadline (http://ourenvironment.berkeley.edu/graduate-programs/admissions/), but if not filled in 2016, this and additional positions may be open in 2017.

The Renner Lab, Evolutionary Biology, San Diego State University, is searching for a graduate student with a background or strong interest in molecular evolution, phylogenetics, and bioinformatics. This student could start as early as fall 2016 if he/she makes the December 14th priority deadline (http://www.bio.sdsu.edu/eb/jdapplications.html), but if not filled in 2016, this position may be open in 2017.

Short project  summary (see also this post)

Geadephaga is the largest clade of organisms that use a single homologous gland system to produce no less than 19 distinct classes of chemical compounds for defense. This project will develop a detailed functional and evolutionary understanding of defensive chemistry evolution by focusing on eight species from the four lineages of quinone producing carabid beetles, including four species commonly known as the bombardier beetles, which chemically blast their defensive quinones at extremely hot temperatures (up to 100 °C). Using a multidisciplinary approach, this project will identify and comparatively examine transcriptomes for genes involved in quinone production, elucidate chemical biosynthetic pathways, and describe the genetic architecture of quinone evolution. From gland-specific transcripts candidate genes related to the production of defensive secretions will be identified and gene function will be validated experimentally by blocking gene transcription and looking phenotypic changes in compounds produced and transcription activity in the chemical secretory cells. Biosynthetic pathways of quinones will be confirmed by injection of labeled amino acid precursors and analysis of compounds produced in the beetles’ glands. In order to study the evolutionary history of quinone biosynthesis in carabids we will infer the phylogenetic history of candidate gene families and the tree topology and branch lengths will be analyzed to test whether genes are ancient and shared among taxa, or if gene diversification is recent and specific to certain lineages. We will test the hypothesis that the genes up-regulated in secretory cells during quinone synthesis are closely related to those involved in quinone production in arthropod cuticle. Thus the project will empirically address the well-known, but untested, scenario of how the bombardier beetle evolved its explosive defense abilities. With the bombardier beetle as a model, the project will help develop elementary school level lesson plans on topics in chemical ecology and biological chemical defense evolution that will reinforce the Next Generation Science Standards. Additional outreach materials will be produced including a high-quality children’s book and web-based resources will be produced that target the prevalent misinformation about bombardier beetle evolution found online.

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DIY, heavy-duty, weather-proof UV light and photo-switch system

Perhaps you are like me and need to run a UV light for insects even when it rains, or especially when it rains (think rain beetles). I have chewed through a bunch of the off the shelf UV lights over the years because they are not made to get wet. Neither the ballast nor the photoelectric switch from BioQuip is designed to be exposed to rain. Plastic bags and duct tape can only do so much.

At lest BioQuip is up front about the limits of their gear.

At lest BioQuip is up front about the limits of their gear. “Protect from dampness?” When am I not damp in the field?

Given my need for a ‘rain or shine light,’ I looked at the kind of materials used in off-road vehicles, marine applications and home, 12 volt solar systems to see what was being used to run lights that must stand up to the elements day in and day out.

The system I built has a number of advantages over the pre-made systems; 1. minimum 16 gauge wire for better flow of current and less heat, 2. fully sealed aluminum circuit box protects the ballast from water and acts as a heat sink, 3. in-line fuse protects ballast from over amping, 4. the marine-grade photoelectric switch is completely weather proof.

The cost of materials is very similar to the pre-made systems, with the DIY one a bit cheaper ($115 v. $134).

Itemized list of items needed to make the UV light system w/switch and costs compared to standard BioQuip equivalent. Shipping and tax not included in prices.

Itemized list of what is needed to make the UV light system w/switch and the costs compared to the standard BioQuip equivalent. Shipping and tax not included in prices.

The BioQuip light + switch system is smaller and lighter. If you need light weight for a long hike then this is not the design for that. If you use cheaper materials you can make a very basic fair weather light cheaper still, but you get what you pay for. There is the advantage that when you buy a system you don’t spend the time and effort to build it and if it fails you might be able to return it for repair or replacement (But not if you leave it out in the rain. Remember “protect from dampness.”)

But if you like to DIY then here is some more information that can help you see how I built mine.

The complete system looks like this. The numbers refer to items in the table above. The wires are quite short for my application, but given the gauge they could be much long and still work very well.

The complete system looks like this. The numbers refer to items in the table above. The wires are quite short for my application, but given the gauge they could be much long and still work very well.

This shows the circuit box with the ballast mounted inside. The red 'a' indicates where I drilled a hole to run the wires through the external mounting holes. This was then filled with marine-grade silicon sealant (10).

This shows the circuit box with the ballast mounted inside. The red ‘a’ indicates where I drilled a hole to run the wires through the external mounting holes. This was then filled with marine-grade silicon sealant (10).

In order to hold the ballast firmly in the circuit box I made a small clip out of sheet aluminum (c) and used the tab on the ballast (a) to hold one end and the internal grounding screw (b) to mount it to the box.

In order to hold the ballast firmly in the circuit box I made a small clip out of sheet aluminum (c) and used the tab on the ballast (a) to hold one end and the internal grounding screw (b) to mount it to the box.

The photoswitch (4) was mounted using one of the box's external mounting hole and the wires were run out the other. Marine-grade silicon sealant (10) was used to seal around the wire exit hole.

The photoswitch (4) was mounted using one of the box’s external mounting holes and the wires were run out the other. Marine-grade silicon sealant (10) was used to seal around the wire exit hole.

The end of the tubes fit perfectly into a cut off standard 50ml centrifuge tube that was drilled for the wires (b). The ends then are wrapped in shot sections of the tube mesh cover and secured with a zip-tie (11).

The end of the tubes fit perfectly into a cut off standard 50ml centrifuge tube that was drilled for the wires (b). The ends then are wrapped in short sections of the tube mesh cover and secured with a zip-tie (11).

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Nevada Carabids: Part 5: Death March to Dead Lake and Heading West

See also part 1, part 2, part 3, part 4

Day 5 – June 13, 2015 [by Riva Madan]

Another storm brewing on the horizon.

Another storm brewing on the horizon.

         Our last day going out in the field at GBNP. We started off by picking up all the traps we had put out. Unfortunately, with the fairly cool weather and scattered rains, many of our ramp traps weren’t that successful; in some we got nothing, others only a bunch of ants. The only common beetles were more Pterostichus, lots of Calathus and Tenebrionidae.

Ramp traps. Beetle activity wasn't a high as we hoped.

Ramp traps. Beetle activity wasn’t as high as we hoped.

After all our trap samples were picked up we went on an adventurous hike to Dead Lake, a small lake well off the main trails and one that we were told dries up in the summer. Given it had been a dry year it may already not be a lake, rather a dead lake, as it is appropriately named.

Hey, Kip. Are you sure you know where you are going?

Hey, Kip. Are you sure you know where you are going?

The road along Snake Creek toward the lake was not open to the public because they were renovating campgrounds, building new trails, and camp sites. It gave us a feeling of being very remote even though the access was easy. When we got to end of the road at the trailhead parking, there were three possible trails to take instead of the one shown on the topo map. Following Kip, we took the trail to the far left, it went up and up, and opened onto a vista of beautiful scenery, but shortly  Kip told us we had taken the wrong trail and were now heading in the opposite direction from the lake. Back down we go.

A beautiful view from the wrong trail if you want to get to Dead Lake.

A beautiful view from the wrong trail if you want to get to Dead Lake.

Right about that time we started to hear thunder and see rain falling hard on the other side of the mountain ridge. Back at the trailhead, we had two trails left to choose from and Kip decided to take the one to the very right thinking it would split into another trail at a point further up. This ended up being the trail that was shown on the map, but not the one that heads directly to Dead Lake (the path not taken), but our trail came close to the lake. Using Kip’s GPS, when we got about 800 meters from the lake and we decided to head off trail and dead-reckon our way to the lake. It didn’t seem too far based on the straightline distance, but what we didn’t realize was how steep the terrain was going to get. Climbing over and walking on top of huge logs and debris, and breaking brush, it kept getting steeper and steeper. It seemed like we were just walking, at times almost climbing, straight up the side of the mountain. Kip was always about 100 feet ahead making it look easy, I was behind him, not too worried, having done things like this before, and Frank was behind me. It was his first experience of going off-trail and hiking up something this steep. By the look on his face, not an experience he’ll soon forget. The whole time we heard thunder in the distance and were hoping it wouldn’t start pouring on us. A big rain could make getting back down to the truck hellish.

Finally, we made the crest and got to the area where the GPS indicated the lake should be. At first we didn’t see any lake. Kip thought it might have totally dried up, but Frank and I thought the area didn’t look like a dried up lake, but open rocky campsite. Having made the hike up, I didn’t want to just leave without finding the lake, regardless if it was dead or not. Gretchen had told us that a flagged trail led to the lake. I was determined to find the flagged trail so we could avoid climbing back down the side of the mountain through the forest.  We searched around and I did find the small lake and then found the flagged trail to take back down. I admit I was unimpressed with the little pond at the end of the big hike. Dead Lake was almost entirely dried up.

The last bit of this year’s life at the edge of Dead Lake.

The last bit of this year’s life at the edge of Dead Lake.

Luckily, it was worth the effort. We found many additional beetle species here and they were abundant. When we were done collecting around the lake, we picked up the flagged trail that would more easily take us back down and as we guessed, it turned out to be the middle trail at the trailhead, the one we didn’t take going up. Despite what seemed like very threatening weather, with thunder and some moments of rain, we collected on the way back. We made frequent stops to looked under the bark of dead, fallen trees. At one deadfall suddenly Kip was very excited thinking that he may have found the rare “stink beetle,” Nomius pygmaeus, (we have never seen him that excited before). Sadly, when he checked it under the microscope, it was only the common smelly beetle Psydrus piceus. But at least it was another species to add to our list for the GBNP.

Searching for beetles under the bark of the dead fall.

Searching for beetles under the bark of the dead fall.

We wound our way back down the trail and drove back to camp. It had been a long day already, but after a quick dinner, we went back out that night for headlamp collecting at a higher elevation near Wheeler Peak Campground. Even though it was quite cold at that elevation, there were a lot of beetles out walking, mostly Calathus, but we found a few species to add to our list.

Day 6 – June 14, 2015 The finale.  


Packed up and headed home! The trip back to California was uneventful, but our work on the project continues. Samples to sort, specimens to pin and lists to make. Between our trip and, mostly from specimens we have looked at in museum collections, we have easiy more than 60 species to add to the list of carabids of Nevada.  

California. That way...

California. That way…

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Patronym, matronym & filionym

"Sad Poncho Night." Orion Will, at Bulburin National Park, Queensland. One image that pretty much sums up the trip for him. Also collected some undescribed carabid beetles here.

“Sad Poncho Night.” Orion Will, at Bulburin National Park, Queensland. One image that pretty much sums up the trip for him. Also collected some undescribed carabid beetles here.

Creative control over the formation of names is one privilege taxonomists have. While most are run of the mill descriptive or locality-based names, patronyms are also very common. Flies have been named for Beyoncé’s voluptuous derrière, carabid beetles named for Governator’s tree-trunk quads and slime-mold beetles for our former (and in my opinion dreadfully bad) president and vice-president (link to article, and here). Lots of species are also named for people that contribute in various ways to the progress of taxonomic science in a more direct or personal way. In my recently published “A taxonomic review, new species and a key to species of Platycoelus Blanchard, 1843 (Coleoptera: Carabidae: Pterostichini)available at Zootaxa (With a key to species!) I had the opportunity to recognize my wife, Chong Hee, for her enduring tolerance of my walkabouts over the last 30+ years and her support (moral and material) in general, with a fine, newly described species from the Cape York Peninsula, QLD. Also my son, Orion Will, who has been my stoic, if somewhat reluctant, field assistant on trips like the one we had across parts of Queensland.

I guess I should have mentioned the land leeches before we left the USA.

The Purple Pub in Normanton, QLD. A place to stay near the type locality of Platycoelus orion.

The Purple Pub in Normanton, QLD. A place to stay near the type locality of Platycoelus orion.

Of the many specimens from our trip, several new species were collected including the then undescribed Platycoelus orion from Normanton, home of the Purple Pub.

 

 

Capture1

 

 

Capture

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Nevada Carabids: Part 4: An approach to Wheeler Peak

See also part 1, part 2, part 3

Day 4 – June 12, 2015 [by Riva Madan]

Snowy peaks in GBNP.

Today was our trip to the higher elevations, reaching about 11,000 ft. It is an easy drive to the trail head at Wheeler Peak Campground and from there we hiked to Teresa Lake. Along the way up the trail, we collected beetles near the melting edges of the snow patches. We were expecting to find Bembidion and Trachypachus here, but at first we didn’t find any beetles at all and started to get worried.  As we continued to get to higher elevation and Frank started to get dizzy from lower oxygen (lol, noob), we started to find the beetles we were looking for. Being so small and fast, it was difficult for me to catch them at first even with an aspirator (aka pooter). Luckily, I quickly got the hang of it and started to find many beetles under the rocks by the lake. 

Teresa Lake, collecting and picnic site.

Teresa Lake, collecting and picnic site.

In the stream running into the lake, we found some interesting cold water beetles that Frank and I hadn’t seen before. After having picnic lunch by the lake, we headed back down to the park maintenance headquarters and washed up in the first and only shower for the trip. 

Scree slope above Teresa Lake.

Scree slope above Teresa Lake.

Frank shows us his sifting moves.

Frank shows us his sifting moves.

That afternoon we rested, took silly pictures, and ate dinner in camp.

Antennae seem like a great idea. Why didn't humans evolve them before?

Antennae seem like a great idea. Why didn’t humans evolve them before?

Once the sun set, we went to Snake Creek  and set up a mercury vapor light sheet and do hand collecting. We were again finding many scarabs and Tenebrionidae, but we did get a few interesting things; Kip and I each collected handsome Carabus taedatus. Some Amara, small harpalines and a some usual Bembidion and Pterostichus were found in the mostly dry creek bed. Though the collecting was slow, our list of species was growing.

Riva and Frank looking for Bembidion in the stream bed.

Riva and Frank looking for Bembidion in the stream bed.

Next blog: Our final (long) day in GBNP.

Posted in Carabids, Entomology | 1 Comment

Nevada carabids: Part 3: Trap Day

See also Part 1 & Part 2

Day 3 – June 11, 2015 [by Riva Madan & Frank Hsu]

Morning breaks in Nevada.

Morning breaks in Nevada.

        Sunrise!! And we got little sleep since the water kept dripping on us inside the tent. On further inspection we found that we actually mounted the rain shield wrong and the shield was actually touching the top of the tent so the water was wicked right through. After more or less drying off our gear and re-erecting the tent with Kip’s help, our first order of business was to set up light traps that might capture night- flying carabids and other insects. We set up three UV-light traps, one each at Baker Lake Trail, Grey Cliffs, and Lehman Creek. The killing agent used to poison the insects worried us a bit, but Kip always handled that stuff. Ironically, the concentration of the killing agent wasn’t even doing a good job at killing insects that flew into the traps. That ends up being a problem, when big moths get in the trap and flap around,  shedding moth scales onto everything.  After getting the light trap set up, we deployed our ramp traps at various locations and different elevations.

Putting out ramp traps. A kind of no-dig pitfall trap.

Putting out ramp traps. A kind of no-dig pitfall trap.

We laid out our handcrafted pipette-box-ramp traps at Snake Creek, along NF road 446, near the Strawberry Creek trailhead and down in Osceola ditch trail. At the NF road 446 site, Kip found a deer skull that had been picked clean by insects and other animals.  We were surprised at how white and clean the skull looked. After the ramp traps were put out, we started to dig holes and put in pitfall traps. The day was going smoothly up until this point, but then massive grey cloud began to displace the open blue sky. What was a nice sunny afternoon took a turn for the worse when sheets of rain began dousing the forest, filling and flooding some of the pitfall traps that we had carefully filled with propylene glycol.

Pitfall trap location along Strawberry Creek. It's getting ready to rain on us.

Pitfall trap location along Strawberry Creek. It’s getting ready to rain on us.

By the time I got back to the truck, literally everything was wet. Kip probably got the worst of it as he headed out to collect DNA samples of Pterostichus protractus from the forest right as the rain became a downpour. We were lucky the rest of the trip wasn’t like this. From here on out, the nights were clear (which made also made it cold) and the sky was filled with an amazing show of stars, just like Gretchen had  mentioned earlier.

Putting out traps near Gray Cliff.

Putting out traps near Gray Cliff.

Next post, up to the high country.

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Nevada Carabids: Part 2: Great Basin National Park

See also- Part 1

Day 2 – June 10, 2015 [By Riva Madan]

Today our primary objective was to reach Great Basin National Park.  Along the drive there, we saw stretch after stretch of flat, brown landscape, with mountains in the distant backdrop. It honestly looked like we were passing Area 51, which was a bit south of our path, or where they could dump radioactive waste from nuclear power plants without anyone knowing (sorry Nevada); at one point Frank thought he saw some kind of large vehicle rolling in the far distance on the flat desert land, but it turned out just to be a dust cloud mirage.

A long view across Nevada.

A long view across Nevada.

        We arrived at Great Basin National Park and were greeted by Gretchen Baker, an ecologist at the park, who gave us a map to get us around the park and told us a bit about the area, some highlights to look for (like the awesome starry nights) access and habitats.

Our campsite in GBNP

Our campsite in GBNP

After setting up in the Baker Creek Campground, on his first adventure out to find the toilets, Kip found a Rhadine (a genus of fairly uncommonly collected beetles that includes some well-known species that are cave dwellers)  inside the restroom. Perhaps we can think of getting this fine beetle as compensation for the previous night’s poor carabid catch. As the night moved in, we donned our headlamps, fired up our vials, and brandished our tools and headed out collecting on a trail close to our camp. Since it was right after the “Rhadine hype”, we were all anxious to find more; however, we found mainly Pterostichus protractus, which turned out to be one of the most dominant species in the park. While peeling bark to look for beetles, we accidentally opened revealed a group of sleepy hornets hiding under the bark. Luckily, they were all inactive so they didn’t react much, but we got a nice adrenaline rush. We carefully tucked them back under the piece of bark and moved away as quick as possible. We enjoyed seeing bats flying around us until one almost collided with Frank’s headlamp as he looked up to see what was making the fluttering noises. The night was cut short by cold drizzle. We headed back to camp to retire for the night; it was then when Frank and I realized: 1. how bad our tent was, and 2. how much we sucked at erecting tents. Water started to ooze in from the seams and drip from the roof. We could only think about how wet this night might get.

Frank and Riva at the camp lab/dinner table, one sunny afternoon in the GBNP

Frank and Riva at the camp lab/dinner table, one sunny afternoon in the GBNP

GBNP, a view of the high peaks.

GBNP, a view of the high peaks.

More to come in Blog 3.

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