The Joshua Tree Genome Project

Hi all! This is Olivia. I am part of a 4 person intern team here on the Mojave Desert, NV working with the USGS on the Joshua Tree Genome Project.

(Check the JTGP out here: http://joshuatreegenome.org)

The mighty Joshua Tree (Yucca brevifolia)
PC: LAD

This project is in collaboration with a handful of academic partners from all over the States and our mentors here in Nevada are among the Principle Investigators because they were some of the first scientists to ever investigate the life cycle, reproduction,
demography, and the effects of climate change on Joshua Trees!

So, Why the JTGP?:

JTs are an icon of the Mojave, provide food for a large range of desert organisms, and have an incredible relationship with their obligate moth pollinators. Both organisms have a long co-evolutionary history together which is known to result in JT population differentiation. Given the changes in climate that are projected for the Mojave and surrounding areas, the JT is now also going to be facing selection based on abiotic factors.
Therefore, the JT Genome Project was created with the goal of examining the JT’s local adaptation to climate, with the purpose of exploring the primary source of selection across populations (climate [abiotic] vs. pollinator driven population differentiation [biotic]). This will be done by identify ecophysiological traits that determine seedling tolerance to climate change and the genes that structure these traits (Project Proposal, 2020). Crazy cool! It is a multi-year study and we have the good fortune of being here right at the start. Oh, and of course, this project also involves sequencing, for the first time, the JT genome.

Our role as CLM interns:

Here at the USGS, we will handle all logistical and practical matters related to the establishment and monitoring of the JTs. This means planting and growing more than 3,000 JTs in our local greenhouse which will then be replanted at four different
common garden sites throughout the Mojave. These four sites represent both the extremes and norms of climate existing across the Mojave. We will then have the opportunity to collect preliminary data and even do some experimental work.
These common garden JTs will be the subjects in genetic analyses and physiological assessments that will be occurring in later years of the study. The work of the USGS and our role as CLM interns is paramount to the establishment and future success of this amazing project.

Fruit of a Joshua Tree

Kicking it off:

This week (among orientations and wrapping up paperwork) we worked on counting and cleaning JT seed collected from a multitude of populations and individuals. This counting and sorting of seed is necessary for the next step: planting!

An opened JT fruit-some aren’t is this nice of a condition. Predation by the moth larvae and other grub is common.
Myself (left) and my co-intern Michele (right) working on seed cleaning and counting!

Counting seed was a great opportunity to see the range of populations we will be working with and the number of individual trees that are a part of this study.
We are so excited to start planting and working in the greenhouse next week-those 3,000 JTs are calling us!

The black seeds are mature and full while the white/tan ones have been aborted and are empty. Some fruits had 500+ seeds while others only had 20!

Until next time,
Olivia T.

A Stormy Welcome

Hello from Alamogordo! 

My name is Julie and I am one of two CLM interns working at the Lincoln National Forest in the Sacramento Mountains of Alamogordo, NM. We arrived in New Mexico back in June, and because of COVID-19 had to quarantine for two weeks. But since then we have been able to be out in the field almost every day and have not had many COVID related issues because of the outdoor nature of the internship. 

Using a GPS and our own two feet, we conduct botany surveys by systematically moving through areas of the National Forest searching for and recording locations of different rare plant species with the hopes of protecting as many of their populations as possible. Some of the plants we have been focusing on are Tall milkvetch (Astragalus altus), Wooton’s alumroot (Heurchera wootonii), Wooton’s hawthorn (Crataegus wootoniana), and Sacramento Mountain Thistle (Cirsium vinaceum). 

Sacramento Mountain Thistle (Cirsium vinaceum) 
Wooton’s alumroot (Heurchera wootonii)

The beginning of July signified the beginning of the New Mexican monsoon season, which brings big thunderstorms into the mountains almost every afternoon from July-September.

A few weeks ago, Emma, my co-intern, and I were in a new survey plot area of 6,000-acres. This was our first big survey plot that was not along a trail, so we were eager to start tackling this massive area and find some rare plants. When we got out to the survey area, we discovered it was rocky and dry, populated by juniper and piñon pine. We were up on top of a peak, in relatively exposed area with very few tall trees, when clouds roll in and we hear the rumbles of thunder. Staying off the tall, exposed peaks, we kept surveying, even when the rain started. The road that we had taken to reach this remote area was a dusty, rocky road that would more or less turn into a mud slide in the rain. We became increasingly aware of this fact the heavier the rain got and the longer we stayed out there. 

Emma in the rain at the start of our day (I know it doesn’t look that rainy in the photo but trust me it was.)

As the rain increased, the small dirt roads became more flooded, and the lightning flashed overhead, we were forced to call it for the day. So, we climbed in our truck and started to inch our way out through the muddy roads. Eventually, after moving at a snail’s pace through the mud, we made it out safe and sound (though very damp) and still got a good start on our survey plot that day.

What a great introduction to the monsoon season and the big weather in the Sacramento Mountains! 

The First Month

Hello from Alamogordo, NM! My name is Emma and I am wrapping up my first month as a CLM botany intern working with the Forest Service in the Lincoln National Forest located in the Sacramento Mountains of southern New Mexico. It has been a fun but unpredictable couple of weeks as New Mexico requires a 14-day quarantine for out of state visitors due to COVID-19. My fellow intern/roommate Julie and I had to keep ourselves busy with various virtual trainings and many hours spent studying the rare plants in the region from keys and guidebooks. We were so excited when we got to start heading out into the field after the two-week quarantine was over!

The Lincoln National Forest!

The original intent of our internship was to validate a habitat suitability analysis for rare plant species in the Lincoln National Forest, however, COVID has delayed some aspects of the model and so, for now, we are focusing on completing large scale surveys of areas that have proposed trail maintenance and restoration plans. The Lincoln National Forest is home to some amazing rare plants, such as the chlorophyll lacking Arizona coralroot (Hexalectris spicata var. arizonica) and the tiny Ladies Tresses orchid (Microthelys rubrocallosa). The time period following our quarantine was filled with tours of the forest and visits to some restoration sites with staff ecologists and hydrologists. It is more challenging than usual to meet other forest service employees, however being outside in the field helps to avoid some COVID restrictions.

One particularly fun outing we had in June was to check out some of the protected areas for rare wildlife species in the Sacramento Ranger District. There are three major districts in the Lincoln National Forest and each has different rare plants and animal species. While Julie and I primarily work in the Sacramento District there is also the Smokey Bear District (the original “birthplace” of Smokey Bear) and the Guadalupe District. The Sacramento district is home to the Mexican Spotted Owl, the New Mexico meadow jumping mouse and the Sacramento Mountain salamander. We were able to hike out with the seasonal crew that was completing wildlife monitoring for the summer and see some of the animals. While I am definitely a plant person, it was interesting to see how different biologists operate in the forest.

A Sacramento Mountain salamander

Over the past two weeks we have started going out on our own to survey for rare plant species in areas that are a part of the South Sacramento Restoration Project, a large scale forest management plan currently underway in the Lincoln Forest. These sites have proposed restoration plans and it is important to gather information on what rare plant populations exist there (or don’t) in order to evaluate the potential environmental impact of treatments. We have also gained some experience in writing reports on our surveys as well as working with GPS and habitat data. So far it has been a great learning experience and I can’t wait to see what the rest of the internship has in store!

Bye-bye Bend!

My time in Bend, OR has been an amazingly fun adventure. Taking a leap of faith and moving out west all the way across the country was one of the best decisions I could have made for myself. I got to see so many different parts of the country and explore all new kinds of territory.

I think a large part of what has made my time in Bend so enjoyable is my job. I have truly enjoyed working at the Bend Seed Extractory. I have learned so much professionally and gained so many skills which pertain to the field I want to pursue. A few examples include: species identification from looking at the seed (I can’t do this with a lot of species, but I have learned a few), seed anatomy, how to process seed, and I’ve learned so much about west coast flora and fauna. Professionally, I have learned what it is like to work for the Federal Government.

My expectations for this internship were beyond exceeded. I really did not know what to expect when I moved here and started my job. To be honest, I didn’t even understand what my job was. I mean what is a “Seed Extractory”? On my first day, I went through an orientation process and learned so much new information (just on that first day!). I didn’t even know a place existed that would process seed for you. In addition, my co-workers immediately welcomed me as a part of the crew. They made OR feel like home and became more than just co-workers but my friends.

In conclusion, I have loved every part of this experience and highly recommend taking a leap of faith, moving to a foreign location and participating in the CLM program. I am excited to start my cross country road trip back home this weekend and will definitely miss my life in Bend!

Lastly, I leave you with a lovely view of the “Sisters”. My everyday view that I will surely miss. 🙂

What A Long, Strange Field Season It’s Been

2019 has been a whirlwind. From wrangling hiring paperwork during a government shutdown to carefully doling out ice water from the thermos in 104° heat, there were trials and tribulations the entire way. This past year, I’ve bounced between four different funding sources, but my primary focus has been the Rare Plant Monitoring Program out of the BLM – New Mexico State Office. This program works hard to develop datasets and protect species before they get federally listed. This crew, based out of Santa Fe, monitors species in every field office of New Mexico. We spent so much time on the road that we listened to the entire Lord of the Rings trilogy on Audible before mid-season reviews!  

Some of the rare species we got to spend time with, from top left: Eriogonum gypsophilum, Astragalus gypsodes, Amsonia tharpii, Coryphantha robustispina ssp. scheeri, Justicia wrightii, Linum allredii.

We read 70 previously established plots and constructed an additional 29 new plots. These permanent transects are used to collect baseline demographic data for these species: what is recruitment like? What is mortality and lifespan for an individual? What reproductive effort is being made by individuals? By collecting this type of data over five or ten years on rare plant species that occur mostly on BLM land, the Botany Program can better inform management practices to protect these species. 2019 was the fourth year of this program, and a lot of species are still being added and kinks are being worked out. This made for an interesting season in which every week we were facing new challenges. Throughout this season, I developed rigorous monitoring methods, improved my plant ID skills, and dove into the wonderful world of geospatial data. It’s deeply rewarding to know that these species that I got to know so intimately have a brighter future because of our work.

Calisthenics at the daily Stretch and Safety meeting before reading an Echinocereus fendleri var. kuenzleri plot.

Since reading our last plots in November, we’ve been working on reporting and analysis for the plots we’ve read. This has been a wonderful opportunity for me to relearn R. Though I love to hate R, it’s a crucial skill for graduate programs and employment, and has made for really robust reporting in the Rare Plant Monitoring program. My crew lead, Lauren Bansbach (featured triumphantly holding an Agave above) is staying on for another season with the Rare Plant Monitoring program. I can’t help but feel jealous and sad that it’s over so soon.

Reading a plot in the Land of Many Uses.

Mike Beitner
Bureau of Land Management
New Mexico State Office

National Parks meet Extractory

Life at the extractory has been busy, busy, BUSY. Before Christmas, we received over 600 lbs of seed from Arches National Park. This order was to be processed and shipped out before the end of January. Though this is a lot of weight in seed, the order only consisted of 6 species / lots. They are as follows: Artemisia filifolia, Chrysothamnus nauseosus, Sporobolus giganteus, Atriplex, Machaeranthera, Krascheninnikovia lanata and Artemisia tridentata. I’m unsure if these species names mean anything to you…but if they do… you’re welcome. 😉 This seed is going to be used for a restoration purposes and planted around Wolfe Creek at Arches National Park. The seed will be planted using a process called, hydroseeding. This is where the seed material is mixed with a variety of organic matter and sprayed out of a large hose in the desired planting area.

In case you don’t know what Arches National Park is / looks like, here is a pic!

Image result for arches national park
https://www.visitutah.com/places-to-go/parks-outdoors/arches/

I was in charge of extracting the 211 lbs of Atriplex that we received. This was, by far, the largest order I’ve ever processed at the extractory. I even got to learn how to use a new machine, the BIG brush machine (compared the the small brush machine that I am accustomed to).

Big brush machine!

It took me almost three whole days to run the seed through this machine and then to clean everything up (as I made a HUGE mess).

In addition, I also processed the Krascheninnikovia (aka Winter Fat) and the Machaeranthera. We received a little over 50 lbs Winter Fat and 25+ of Machaeranthera. I was in charge of running this seed through the Missoula (a machine that I have talked about in previous blogs). Because Winter Fat is so fluffy it takes multiple runs through the machine and does not flow through the machine by itself (so I manually pushed it). Machaeranthera, is an Aster and has a pappus that needs to be removed, however, it can be pesky to remove and also required additional runs in the Missoula.

While it was tedious, time consuming, and seemed endless, the reward and pleasure I found in finishing both of these lots was enormous. Looking at the final product after putting in so many days of work made it all worth it. Here are some pictures of the final products all neatly packages and ready to be shipped back to Arches!

Here is the Atriplex! Four huge bags full.
The middle bag- “ARCH19-02” is the Winter Fat and “ARCH19-03” is the Machaeranthera.

Starting in February we will begin to process seed for the, Petrified Forest National Park. This seed will be used for roadside restoration purposes. This seed will go towards re-vegetation efforts in order to control non-native / weedy pants and increase genetic variation of native species.

Stay tuned for my FINAL CLM blog coming in February.

It’s Bend Fun, Y’all

In recalling the goodbye’s of my past, this one is received unwelcome, unwanted, and unfortunate. Never before can I call back to a parting of ways that even the thought is difficult to accept.

Some adapt to change at a pace far quicker than some, others need heavy investment of time before they gain traction. For me I’ve found, especially in this exact moment, that the duration of the CLM positions is the precise amount of time I need to not only get in, but enjoy the groove. 5 and a half months of myself invested somewhere I’ve never been – somewhere that 5 and a half months ago I never pictured myself becoming enamored with.

Bend speaks for itself. In more ways than can be stated, it’s more than I expected. But as they’ve all supposedly said, it’s not the place, it’s the company. Well, they were right.

I can’t begin to claim I found myself out here without giving unwavering credit to the folks I worked with. My supervisor, coworkers, peers, etc, all quickly become synonymous with none other than – friend. I can say I’ve never developed such a favorable dynamic in any prior work environment. And that is said with confidence.

My time at Bend Seed Extractory has provided invaluable experiences, opportunities, and responsibilities – all of which, I believe, leave me a greater asset.

Saying Goodbye

Greetings!

With all of the experiences I’ve had and the people I’ve met over the last 6 months, it is a wonder why I struggle to find the right words in my final blog post. I believe that my reluctance to leave and unwillingness to accept that this is my last day is the main reason.

Just yesterday, I was in the office making sure that a set of herbarium vouchers was going to be shipped properly. Even then, it felt like a long time before I would have to leave the field office and the country that I’ve grown so accustomed to in the previous months. Earlier this week, one of the range staff brought me to the field to show the air quality monitoring acid deposition and mercury levels in the water around the foothills and southern Wind River Mountains that he does on a regular basis. It is amazing to see such modern technology in equally remote areas–some of which are entirely solar powered (and have been since the 80s). As shown in the picture, there is a sensor that, when prompted by moisture, lifts a lid on and allows precipitation into a container. Data from this sensor and the corresponding precipitation is stored in a nearby computer (the cylindrical container with the hoop of flapping pieces around it). This data is then collected via a USB drive or Bluetooth! I have no idea what I expected air quality monitoring to look like, but my mind was a bit blown to say the least. Along the way, a black widow spider even walked up to say hello! I could not have asked for a better final day in the field.

This field season has been a blur, but I can say with certainty that it has been a success. My co-intern and I had a target goal of collecting 20 different species of native seeds, with 20,000 seeds per species. We ended making 27 collections, many of which (we believe) surpassed 20,000 seeds. My favorite collections have been Penstemon paysoniorum (because of its initial elusiveness and plump fruits), Hedysarum boreale ssp. boreale var. boreale (because of the location on a hillside and the golden sheen of the seed pods), and Gentiana affinis (because of its tiny papery seeds and the location of my favorite wild horse area). During this time, I have greatly improved my plant identification skills, as well as learned many new species of plants from this area. I was surprised to learn that there is quite a bit of overlap of genera between the basin and foothills of Wyoming and many areas of the Midwest where I have collected seed previously.

And I couldn’t finish my final blog post without at least mentioning my co-intern Maggie. I could not have picked a better person to spend so much time with. In many ways, we could not be more different. However, we have many of the same tendencies and were an excellent match. We laughed, worked, complained, succeeded, and failed together. This season would not have been the same without her.

This internship has also allowed me to visit states I may never have gotten a chance to see otherwise. Idaho, Colorado, Utah, and of course, Wyoming are now all on my list, and I would come back to any of them.

On a personal and professional level, this internship has been invaluable. I can’t now imagine what my life would have been like having not had these experiences. This may sound dramatic, but having never been out west, and never to Wyoming, I feel that I have learned more than if I had spent multiple years in the Midwest.

I can truly say that I’ve been active and learning (and have people willing to teach me) up until the end. I cannot thank the people in the Lander Field Office enough (and especially my mentor Emma), and for having the opportunity to learn even a sliver about what the BLM does and the country it oversees.

Missing Wyoming already!

Tis the Season

Ho, Ho, Ho and hello!

So, Bend is definitely starting to feel like home. However, with the holidays approaching I will be heading back to Virginia for Christmas! I am super excited to see my family, friends, and be back in the Shenandoah Valley.

I figured I would use this blog post as a summary of my time and work at the Bend Seed Extractory. Our assistant manager recently went on detail and the person who usually works with me in extraction has taken on her position while she is away. This has left me to be the only person in extraction most days. At first, I found this to be very intimating (as I am still somewhat new and lack knowledge compared to more experienced employees). However, as time began to pass, I became more confident in my extraction skills and begun to have a new found faith in myself that I know what I am doing.

Here is a picture of the room that I work in everyday (usually alone, but some days people join me :-)) We call this room, “the big room”.

As you can see, we have many different types of machinery such as eclipses, Missoulas, brush machines and sieves of every size you can imagine. I recognize all of those names mean nothing to you, but they are vital in our process. The two machines I predominately work on are the Missoula and small brush machine.

The machine above is the Missoula. This machine was originally used to break down conifer seeds. However, we have found many new purposes for it and actually do not put conifer seeds in it at all anymore. The Missoula mainly is used to reduce inert material through its vaccuum system, break down flowers in order to extract and isolate seeds, and lastly to remove pappus off of aster species. I would say the Missoula is most often used for pappus removal. This machine is made up of three rubber flaps, a mantle and an air vac system. The flaps move clockwise (at a speed of your choosing) and rub seed against the mantle causing seed to be released from flower heads or removing pappus. Then the air vaccuum system is used to suck up material such as the pappus that was removed or useless flower parts.

The next machine that I use frequently is the, small brush machine (apologies for the horizontal picture). This machine is mainly used for grasses or seed that comes enclosed in a capsule. Inside are three brushes which move in a circle against a mantle to work the seed. The mantle size can vary. For example, if you are working a lot that has a lot of flower material, you can select a mantle that the seed fits through. This way the seed goes out the bottom of the machine and through the mantle and all of the unwanted material continues to come out of the end of the machine. Another use for this machine is to reduce awns on grass species. Awns, are hairs that are attached to numerous grass species and reduce the flow of the seed. We will put these species in the brush machine and get the awns to come out of the bottom as the brushes rub the seed against the mantle and the seed will come out at the end.

Anyway, hope you enjoyed my short summary and update on life at the extractory.

Have a happy holidays!!!

A Peek into Lucky Peak

Who doesn’t love a field trip?

Recently, a fellow CLM Intern, Cassie, and I, were given the opportunity to attend one. No, not to an aquarium, or a zoo full of exotic animals (however, we managed to find one in our off-time), but to a conference held at a location many may call a zoo. From the pensive, to the pretentious, the sober, and to the not-so-sober – none other than the folks with the magnificent blue turf: Boise State University.

After the fairly sizable drive to Boise, we made a stop about 20 minutes before we reached the university. Here, the closest operation similar to our own, was the impressive Lucky Peak Nursery.

The Lucky Peak Nursery is a unit within the Boise National Forest. Much like our own, clients will send seed, which Luck Peak will produce the seedlings. And this is no feat to bat you eyes at either…Over 3 million sage brush and bitter brush seedlings establish their roots here. The seeds are sown, harvested, packaged, and shipped back to the client come spring where they’ll embark on a new journey to be planted for restoration projects.

The importance of these seedlings are more paramount than ever. Aerial seeding is utilized for similar projects, yes, but the success rate of seedlings is arguably higher. So, efforts such as these can supply seedlings that could thwart the efforts of invasives taking over recently burned, disturbed habitats, (connecting back to my last post where we actually planted the same plugs at a burn site). Lucky Peak is an ally though ought to be held with high regard.



I must say though, I feel fortunate to have found the opportunity to gain the experience of this visit. Truly seeing the behind-the-scenes efforts, which take place to ensure restoration efforts are supplied with viable, worthy products, is a glimpse many may not receive. Yes, many of us have taken part in said restoration projects, but have we seen where it all (in this case sage and brittle brush) comes from?

I’d like to add that given both Cassie and I began our internships much later than most of the other CLM interns, we were unable to attend the workshop hosted at the Chicago Botanic Garden – such a shame! If the garden isn’t enthralling enough, Chicago has more reasons than you can count to enjoy. I was disappointed to miss out, but I think its safe to say we found our own North-West land of deep-dish pizza and Chicago dogs. But this one comes with seeds – and I’m not talkin’ poppy seeds either.