Application of the collection’s biodiversity data to the VertNet database

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Mary Casillas, Undergraduate WFSC Student

Undergraduate WFSC Student Mary Casillas next to the ultra-cold freezers that house our genomics collections at the BRTC.

During the summer and fall of 2017, I interned at the Biodiversity Research and Teaching Collections (BRTC) at Texas A&M University (TAMU). The BRTC is a natural history collection, housing specimen data from a variety of organisms from all over the world. I have helped organize data and materials for the collections so that this information can be made available to the scientific and public communities. This material can be organized in files that are sent to a large collective database, VertNet. VertNet is an online database that disseminates biodiversity data from bio collections all around the world.  The database provides tools for collaborating, sharing and publishing biodiversity data. Through VertNet, anyone (including other collections and institutions) can access the data from TAMU BRTC for their own use. VertNet also trains users to practice quality biodiversity data curation and publication such that these important data can be easily used across a variety of platforms.

The process of databasing BRTC data:

My internship at the BRTC involved organizing and documenting ancillary data from specimens so that these data could be added to the BRTC databases and VertNet. Ancillary data are things taken from individual specimens, such as parasites or tissues and DNA for molecular work. I began my work in one of the -20 work freezers. These freezers house tissues, DNAs and parasites that have not been organized or entered into the collection databases and are called work freezers for this reason (the samples need to be worked on before being stored permanently in the collection). Tissues are generally samples taken from specimen’s liver, kidney, heart, ear or feces and DNA samples are usually derived from tissues samples through an extraction process in the laboratory. Parasites normally consist of ectoparasites such as ticks, fleas, or lice- that were taken from the specimen’s body.

Each type of ancillary data is located in a small tube, with the collector initials and numbers written on the outside of the tube. Tissues, DNAs and parasites are grouped in together in separate boxes for easier organization and access. To organize each type of ancillary data, tubes are organized sequentially by collector initials and number in freezer boxes with the small 9X9 grids that keep the tubes in order. Once a collector has filled a box sequentially with samples, the box is labeled with collector initials and a number and moved from a work freezer to a -80 freezer for permanent storage and the data (type of sample and box number) are transferred to the collection databases. Racks are utilized to organize freezer boxes within the -80 freezers and there are maps posted on the outside of each freezer detailing the exact locations of each freezer box. The large -80 freezers provide quality preservation of the samples, and should be opened as little as possible to prevent humidity from entering the freezers, which could cause long-term inefficiency and damage the samples and shelving.  All data from the specimens, obtained from collector catalogs, are formatted for the BRTC databases and then fed to  VertNet for screening. Once the data formats are acceptable by VertNet, the submission of biodiversity data will be added to the free domain for anyone to access.

How can the scientific and nonscientific communities use the BRTC data?

Once the data are accessible in multiple databases, both scientific and non-scientific communities can freely access the information. These communities could use the search engine to look up a specific species of interest, and find data that the BRTC (or any other biocollection) has collected for specimens representing that species. Advanced search options are available for users to search for a specimen by catalog, institution and much more. A collector can also search for specimens that have tissue data, georeferencing information, or media available. This sharing of information ensures that every bit of data collected is being applied to its full potential.

oVert Thematic Collections Network

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Texas A&M’s Biodiversity Research and Teaching Collections will play an integral role in the new oVert Thematic Collections Network (TCN). The project is supported by a $2.5 million National Science Foundation grant and will utilize specimens from the BRTC and other collections to make data-rich 3-D images available on-line. Texas A&M University is one of 16 institutions to be involved in this groundbreaking project, which will scan and make available museums specimens in a unique way – capturing not only external, but internal morphology. In total, 20,000 specimens representing more than 80 percent of existing vertebrate genera will be scanned utilizing non-invasive CT scanning technology. Texas A&M University will serve as a scanning hub for larger specimens, utilizing resources at the Texas Institute for Pre-clinical Studies and the A&M Libraries.

This project will begin later this fall, more details can be found within the Science article here: http://www.sciencemag.org/news/2017/08/new-3d-scanning-campaign-will-reveal-20000-animals-stunning-detail

 

Dr. Ira F. Greenbaum Collections

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Story by Student Intern Rick Orozco

I had the opportunity to sit and talk to Dr. Ira F. Greenbaum about his research on Peromyscus maniculatus (deer mice) in the Pacific Northwest region. First, a little bit of background on Dr. Greenbaum: he attended Hofstra University where he acquired his Bachelor’s degree in Biology in 1973. After that, he worked on his Master’s and PhD in Zoology at Texas Tech University in 1975 and 1978, respectively. He then joined the Department of Biology at Texas A&M University and is currently Professor and Director of Lower Division Instruction where he is enhancing the education of undergraduate students.

When asked why he thought the Peromyscus study was important, Dr. Greenbaum mentioned how the original research was designed to do something very different. When he started his research, during the time of his PhD, all the deer mice in the Pacific Northwest were one species, Peromyscus maniculatus. Dr. Greenbaum’s research focus was on the chromosomal structure of the mice, such as short and long arms and how they influence chromosome pairing and how they segregate during meiosis. One point that Dr. Greenbaum mentioned dated back to Barbara McClintock’s work in the 1930’s, which revealed when you have heterozygosity for inversions you tend to have duplicated and deleted products during meiosis. This is problematic because individuals affected with this are generally less fit with low reproductive success due to half of their gametes being unbalanced. Dr. Greenbaum started finding frequent pericentric invesions within populations of Peromyscus maniculatus and wondered how this could be occurring? How could you get what’s called a meiotic under- dominant rearrangement, a chromosomal arrangement that should not be maintained at high frequencies within these Peromyscus populations? A problem Dr. Greenbaum encountered in preparing to answer this question was determining how to establish an experimental design that depends upon populations when you have a mouse that is distributed from the Atlantic to the Pacific and from the Northern Tundra to Central Mexico. Basically, it is difficult to study population genetics when you can’t recognize a population. Dr. Greenbaum solved this by creating the assumption that mice from one island are a different population than those on another island. His hypothesis was that “it’s not that the mice can’t swim, but the fish swim a lot better.”

Dr. Greenbaum sought to test the hypothesis that the type of chromosomal evolution observed in P. maniculatus was driven by genetic drift, which occurs much faster and intensely in smaller populations (i.e., islands) than large populations. What actually happened when the research started was that Dr. Greenbaum arrived at the Pacific Northwest region and discovered not just one species but two: Peromyscus maniculatus and Peromyscus keeni (he had no idea of this prior to the hypothesis). Keeping it short, he mentioned that no hybrids were found so it was clear that these two species were not interbreeding.

So how exactly did Dr. Greenbaum discover that there were two species? He wasn’t sure exactly where he did the first capture of both species but he thinks it was on Salt Spring Island, Canada. Dr. Greenbaum and his crew set Sherman traps in the afternoon, sat around the campsite, ate dinner, had a bourbon or two, and went to bed (to me this sounds like a perfect night). In the morning, the traps were collected and the live mice were placed in cages. What happened next baffled everyone; the mice started fighting one another. Since healthy mice were preferred, they sorted them into groups that didn’t try to kill each other. After some trial and error, they noticed some differences between the two groups: one group was smaller and lighter in color than the other. This conclusion was made with just physical characteristics; fast-forwarding through the entire lab process, bone marrow, hearts, livers, and kidneys provided the last sets of data to support the existence of two different species. Going back to his hypothesis, Dr. Greenbaum and his colleagues found several small islands where both species co-occurred and were both polymorphic for pericentric inversion at high frequencies (50%) for chromosomes 6 and 7. This revealed that genetic drift was not a primary factor in the chromosome evolution or chromosomal polymorphism.

Aside from the actual research, I was also interested in the behind-the-scenes events that weren’t reported in the published manuscripts. Dr. Greenbaum specifically mentioned Harry Sowchhuck a logger who showed them great hospitality by fixing their two flat tires, charging no fees, and then took them home so they can eat, bathe, and sleep. It’s not every day that one stumbles upon a special person like that. Another interesting event was when Dr. Greenbaum and his crew were staying at a motel in Washington. He said that they were thrown out of this motel due to taking live mice into the facility. Imagine what people thought when they saw some random guys getting off a truck carrying cages full of mice, centrifuges, test tubes, microscopes, liquid nitrogen tanks, and much more. Because of that, they started telling people what they were doing before they booked a room. When they told the owner of a motel in the city of Nanaimo, Canada, he said that they could continue but on the condition that they trapped the mice around the motel. Dr. Greenbaum said “we caught more mice around that motel than at many of our trapping localities.”

The way Dr. Greenbaum spoke about his time in the field was stunning. His tone showed me that he absolutely loved every moment out in the field. A good estimate of the time Dr. Greenbaum spent in the field was about 30 years, which included his time in Latin America. He said that there will always be difficulties during those trips such as getting a cold, food poisoning, and severe weather. Simply put, “stuff happens.” When I asked for Dr. Greenbaum’s top 5 favorite trips, he could not come up with a list because every trip was his favorite, except for that one trip with the extremely hot summer in Baja California. I was a little anxious before doing this interview since this was my first interview and I had not met Dr. Greenbaum previously. However, it turned to be a fun and great learning experience. Dr. Greenbaum is an easy-going, family oriented, big-time fisherman who does his best every day to make a societal contribution by helping young people educate themselves and get to where they want to go in life. He had always wanted to be a college professor and run a graduate research program. In fact, he loved his college years so much that he decided he was going to stay on a college campus for the rest of his life. When asked to describe his overall experience with his career, Dr. Greenbaum said “I can’t. I love it. It’s what I do.”

Read Rick’s reviews of two of Dr. Greenbaum’s research articles: Hogan et al 1993 summary Allard and Greenbaum 1988 Summary

New species of clingfish discovered!

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Dr. Kevin Conway, Curator of Fishes at the Biodiversity Research and Teaching Collections, and Dr. Phil Hastings, Professor and Curator of Marine Vertebrates at SCRIPPS, describe a new species of clingfish from the Los Frailes canyon in the southwestern Gulf of California. This group of fishes is best known for occurring in rocky intertidal and shallow subtidal reef areas in the western Atlantic. The discovery of this new species the “Canyon Clingfish” is additionally noteworthy because the specimen was collected at a greater depth than most species of this group are known to occur. Read the full description here.

Canyon Clingfish (Gobiesox lanceolatus)

Canyon Clingfish (Gobiesox lanceolatus)

Collection of Birds at Biodiversity Research and Teaching Collections adds a rare bird and reaches 24,000 specimens.

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African sunbird specimens being integrated into the collections at the BRTC.

African sunbird specimens being integrated into the collections at the BRTC.

The Collection of Birds at the BRTC now contains over 24,000 specimens!  Historically the collection has focused on specimens from the United States and Texas (63% of the collection) and Mexico (14%), but it also includes specimens from 64 additional countries.  Over the past eight years, the collection has grown from ca. 14,500 specimens, and has added material not only from Texas, but from expeditions to Armenia, Benin, Democratic Republic of the Congo, Italy, and South Africa. In fact, 5% of the collection is now from South Africa. These international expeditions have been related to research being conducted by Dr. Gary Voelker (Professor and Faculty Curator of Birds), his graduate and undergraduate students, and BRTC staff. Because of these expeditions, the collection has not only grown in numbers, but in species diversity as well. This diversity is represented by 1,662 species, from 785 genera and 163 families. The majority of specimens are prepared as study skins; however, the collections include nearly 1,950 skeletons, 315 fluid preserved specimens, 434 egg sets and 3,201 open wings. The Collection also maintains a rapidly growing collection of tissues (over 8,200) and blood samples associated with voucher specimens.

Canyon towhee specimen from Sierra Diablo Wildlife Management area in the Trans-Pecos region of Texas, prepped in the field to be added to the collection of birds.

Canyon towhee specimen from Sierra Diablo Wildlife Management area in the Trans-Pecos region of Texas, prepped in the field to be added to the collection of birds.

Since the inception of the BRTC, research projects by faculty, students and staff at Texas A&M University have provided most of the material in this collection; however, the collection has also grown through acquisition of the ornithology collections of Guadalupe Mountains National Park, Austin College, Southern Methodist University, Midwestern University and the University of North Texas. And, we have a network of people that salvage specimens for us.  Our fantastic cadres of interns and volunteers have been instrumental in helping us deal with this influx of specimens, via preparing specimens and assisting in collection curation.  As the only active ornithology collection in Texas, in terms of research activities, we anticipate continued growth in numbers and diversity that will not only benefit research, but the many Wildlife and Fisheries Sciences students taking courses that extensively utilize the collection.

Specimen number 24,000 is a federally endangered Whooping Crane. This specimen is one of two birds illegally shot in east Texas earlier this year. We’ve been working with USFWS Special Agents to ensure that these specimens and their data are made available to the scientific community thru accession into BRTC. This specimen represents only the 37th specimen of Whooping Crane from Texas, with a majority of the other specimens dating from the late 1800’s.

Whooping Crane received from USFWS makes specimen number 24,000 in the collection of birds at the BRTC.

Whooping Crane received from USFWS makes specimen number 24,000 in the collection of birds at the BRTC.

WFSC Departmental Newsletter

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Department of Wildlife and Fisheries Sciences Fall Newsletter – check it out here: WFSC Fall Newsletter!

3 New Species of African Forest Robin

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WFSC team discovers three new species of African forest robins in the genus Stiphrornis!

The paper describing these new species has been published online in Systematics and Biodiversity (http://www.tandfonline.com/doi/full/10.1080/14772000.2016.1226978).  The three species are named Stiphrornis inexpectatus, the Ghana Forest Robin; Stiphrornis dahomeyensis, the Dahomey Forest Robin, and Stiphrornis rudderi, Rudder’s Forest Robin.  The latter, Rudder’s Forest Robin, is named in honor of James Earl Rudder, former president of Texas A&M University. The type specimens for dahomeyensis and rudderi (pictured below) are housed in the Collection of Birds at the BRTC. This discovery provides additional evidence that a substantial amount of cryptic diversity exists in Afrotropical forests, which are in need of further study.

 

Rudder's Forest Robin (Stiphrornis rudderi).

Rudder’s Forest Robin (Stiphrornis rudderi).

 

Dahomey Forest Robin (Stiphrornis dahomeyensis).

Dahomey Forest Robin (Stiphrornis dahomeyensis).

Angela Guajardo, Student Intern

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Case Checks

Checking specimens for condition.

Checking specimens for condition.

The Biodiversity Research and Teaching Collections, or the BRTC, at Texas A&M University is one of the largest university based natural history collections in the United States. Home to over a million preserved specimens, the BRTC serves as a worthwhile educational tool for the students of Texas A&M. As a student, I have had the pleasure of working at the BRTC in the mammal division under Dr. Jessica Light. The mammal division of the BRTC is comprised of mammal skin, skeleton, and alcohol specimens that have been collected from various parts of the world (mostly Central and South America, the Gulf of Mexico, and the United States) over many years. The skin and skeleton specimens are housed in museum-grade cases for protection; one of the first tasks I was assigned was to check these storage cases for insect infestations.

Some of the first specimens housed in the collections were from the 1930s. Therefore, Dr. Light and her colleagues in the mammal division have gone to great lengths to make sure each specimen is properly protected so that it remains in good condition for future research. Each museum-grade case physically protects the specimens from the elements (exposure to air, light damage, etc.) and insects such as cigarette beetles that feed on the specimen skins. To further deter insects, moth balls are placed within each case. But, since these cases are opened often, they need to be routinely checked for possible infestations. My job required inspecting each individual skin for live cigarette beetles as well as adding more moth balls to cases when needed. I originally thought I would be able to complete this task fairly quickly. However, I could not have been more wrong.

On average, each case is able to hold about 16 drawers, with some drawers holding over 50 specimens depending on size. Naturally, the cases to which I was assigned were either bats or rodents, so there were a good number of specimens per drawer and it took me quite a few weeks to finish this task. Although monotonous, it was a simple job: if I saw a cigarette beetle, I would squish it between my fingers. If the beetle was dry, then it had been dead for a while and the debris needed to be cleaned out from the drawer. If the beetle left moisture, there could be a possible infestation that would require the entire case to be quarantined. If there were no cigarettes beetles visible on a tray, the next step required examining each specimen for any holes or other signs of infestation. During my case checks, I never came across any live cigarette beetles, but there was one specimen that caught my eye. I was almost finished with my case checks when I found a rodent that had several small holes on the ventral side of the specimen. I did not notice any cigarette beetles on the specimen itself, but I thought it would be best to bring it up to Dr. Light. Luckily, Dr. Emma Gomez, the mammal division collections manager, and I were able to determine the small holes in the specimen were a product of an old infestation and would not require any special attention.

I am very grateful to have had the opportunity to work with Dr. Jessica Light and researchers and staff at the BRTC. During my time at the collections, I have gained valuable experiences working with fragile specimens as well as expanding my organizational skills. As a senior, I am confident my experiences will benefit me in my future endeavors.

Small mammal prep – Student Intern Hudson Berkhouse

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Specimens prepared for the collections at the BRTC.

Specimens prepared for the collections at the BRTC.

My name is Hudson Berkhouse and I am a senior at Texas A&M University.  For the past two years I have been a Wildlife and Fisheries Sciences major (WFSC; or as I like to say, a Wi-Fi-Sci-Guy), with an emphasis on management.  Prior to becoming a WFSC major, I majored in Biomedical Sciences. I changed my major as a sophomore because I wanted hands-on field and lab experience, both of which are heavily emphasized in Wildlife and Fisheries Sciences.  Accordingly, my internship entailed working as a field technician for Dr. Light (http://people.tamu.edu/~jlight2; Associate Professor of Mammalogy at Texas A&M) during the summer between my junior and senior year.  For this internship, I spent the majority of my time collecting biodiversity data at several ranches in South Texas owned by The East Foundation (http://www.eastfoundation.net/).

This work involved trapping small mammals and collecting data from them.  While most of the animals we trapped were ultimately freed, some were retained and prepared as scientific specimens to be installed at the Texas A&M University Natural History Museum, the Biodiversity Research and Teaching Collections (BRTC; https://brtc.tamu.edu/home-2/).  The BRTC is a large warehouse east of campus where over one million animal specimens are housed.  These specimens include birds, mammals, amphibians and reptiles, fishes, parasites, and marine invertebrates from around the world.  BRTC specimens are invaluable and are used internationally for research as well as to teach life history and taxonomy classes at Texas A&M.

The specimens that we chose to retain from the field, to be installed in the BRTC as scientific specimens, had to be prepared in a way that ensures their preservation.  Specimens kept for preparation were carefully and humanely euthanized and immediately stored at freezing temperatures to preserve them until they could be processed.  After they could be transported back to the BRTC, the careful work of specimen preparation could begin.  The specimens were removed from the freezer and allowed to thaw.  When I prepared my specimens, I would first brush them for ectoparasites, which, if any where present, I would collect in a small vial for use by other researchers.  The animal would then be weighed, sexed, and measured.  I would then take a small, round biopsy sample from the ear of each individual as well.  This ear sample would ultimately be used to determine what types of pathogens, if any, the animal was carrying thus enabling researchers to develop a pathogenic profile of the area from which the animal had been collected.

Once the tasks dealing with the external part of the specimen had been accomplished, I could then begin to remove the animal’s pelt and stuff it with cotton and wire.  This had to be done very carefully, following specific protocols, so that the pelt could be retained as close as possible to its original condition.  See previous posts by Noel Lyon (https://brtc.tamu.edu/2015/06/10/small-mammal-preparation-at-the-brtc/) and Stefan Hill (https://brtc.tamu.edu/2015/07/06/mammal-preparation-at-the-brtc-stephan-hill/) detailing the preparation process. Because the collections at the BRTC are used to teach university classes as well as for research, it is important to make sure that all specimens are in good condition.  The animals we collected from the East Properties, for instance, are ultimately going to form a collection specifically intended to present a biodiversity profile of the South Texas region.

 

Specimens installed into the research collection.

Specimens installed into the research collection.

Another important part of the preparation process is the removal of the individual’s organs and the retention of their inner tissues.  Any tissues which are kept are potential data sources for future projects.  Keeping track of these tissues ensures that the maximum amount of data is retrieved from each specimen, making the most of these valuable resources. I usually retained heart, kidney, and liver tissues from my specimens and I placed these tissues in clearly labelled vials stored at freezing temperatures.  The finished product was a stuffed and sewn pelt, an intact skeleton (which had to be left in a cleaning tank for tissue removal; see previous posts by Stefan Hill (https://brtc.tamu.edu/2015/06/03/stefan-hill-dermestid-care-level-expert/)), and several vials containing various tissues for future research.

Specimen preparation is an interesting job, but one that needs to be undertaken carefully and methodically. The two other undergraduates I worked with, Joshua Brown and Hunter Folmar, were extremely helpful and always willing to give me advice, as they both had more experience in specimen preparation than I did.  I would also say that learning how to humanely cull these animals and carefully prepare them as intact specimens was the most important skill I learned during my valuable experience as a field technician.  This is because the preparation process not only taught me how to properly clean an animal but also gave me a much better understanding of mammal anatomy.

Data Collection – Student Intern Hudson Berkhouse

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My name is Hudson Berkhouse and I am a senior Wildlife and Fisheries Sciences major at Texas A&M University.  One of the reasons I was originally drawn to this major was that it combines a thorough scientific education in many wildlife-related scientific fields with hands-on training and experience.  Accordingly, students seeking a degree in Wildlife and Fisheries Sciences must, at some point in their undergraduate years, fulfill an internship that is in some way related to their studies.  For my internship, I was able to work as a field technician and on several other tasks for Dr. Light, a professor of Mammalogy, at Texas A&M during the summer of 2015.

Student intern Hudson Berkhouse.

Student intern Hudson Berkhouse.

The field-based project I worked on was a biodiversity research project in South Texas based at several ranches owned by the East Foundation (http://www.eastfoundation.net/).  During my internship, I traveled with other field technicians to the ranches to collect data concerning the presence and abundance of small mammals.  Because most of the land in Texas is privately owned and therefore difficult to access for research purposes, this project is able to provide important data towards a better understanding of the distributions of wildlife spread across Northern Mexico and Southern Texas.

As I mentioned earlier, my team was concerned primarily with data collection on small mammals, or “smammals” as we affectionately referred to them.  Towards this end, our daily routine consisted of setting Sherman traps in the early evening when it had begun cooling off, retrieving those traps early the next morning before it got too hot, and collecting both data and specimens from the animals we had trapped.

Although every aspect of this process was interesting to me, I specifically want to describe the data and specimen collection process.  When we went out into the field to retrieve our traps in the mornings, we made sure to bring all equipment necessary for gathering data with us.  Collecting the data as soon as possible was important because it reduced stress on the animals, ensured that whatever specimens we chose to retain would be in good shape, and protected the accuracy of our data by reducing opportunities for human error.

 

Perognathus returns to the field after being processed.

Peromyscus returns to the field after being processed.

Some of transects where we trapped were intended to yield data only, whereas others were set with the goal of specimen retention.  Animals found in traps that fell into the former category were weighed, sexed, measured, and freed. During this process we took note of any obvious deformities or ectoparasites that could be found on the animal.  The most important data from these transects involved which species could be found at different locations throughout the ranch. The goal of the latter type of transect (where specimens were retained) was to collect a few specimens of each species, destined for preparation and preservation.  Accordingly, those animals belonging to species that had already been collected were freed, whereas members of the different target species were culled and preserved.  Throughout all of these steps it was impressed upon me that minimizing the stress each animal must undergo, whether they are to be freed or culled, is of the utmost importance.

Part of what made this internship such a valuable experience was the insight into field work it gave me, as well as a much better understanding of what it is to do scientific research in my field of study.  I also greatly enjoyed getting to know my coworkers in an arena outside the classroom.  As a result of my job that summer, I know and respect my fellow students more, and have a much better understanding of the professional aspects of my major.