The Collection of Birds from the Biodiversity Research and Teaching Collections will host an exhibit including original photography, specimens, data visualizations and more at the SEAD Gallery in downtown Bryan, read more here: https://brtc.tamu.edu/collections/ornithology/vitality/
Application of the collection’s biodiversity data to the VertNet database
Mary Casillas, Undergraduate WFSC Student
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
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
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!
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.
Collection of Birds at Biodiversity Research and Teaching Collections adds a rare bird and reaches 24,000 specimens.
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.
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.
WFSC Departmental Newsletter
Department of Wildlife and Fisheries Sciences Fall Newsletter – check it out here: WFSC Fall Newsletter!
3 New Species of African Forest Robin
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.
