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Global Genome Initiative 08/31/2016
DNA Barcoding Borneo’s Biodiversity: A Modern-Day Naturalist’s Journey into the Heart of Borneo A James Madison University (JMU) professor takes his students on an international collaborative adventure to document the amphibian and reptile biodiversity of Borneo. I have always felt I was born about 100 years too late. When I am out doing my fieldwork in the tropics of Southeast Asia, I wonder what it would have been like to be in Borneo with Alfred Russel Wallace in the 1850s–60s. How different would it have been? How similar? What am I seeing that he didn't? What did he see that I will never encounter? As an educator and researcher, I’m engaged in training the next generation of taxonomists, ecologists, and citizen scientists. How do we best do this? First, we introduce them to biodiversity. We challenge them to become observers, to question things, and become problem solvers. We provide them with tools to address their questions and facilitate their exploration of the natural world. Then, we watch with great expectation that they well surpass our efforts and understanding. During the summer of 2016, a team of students and researchers from the Smithsonian Institution, James Madison University (JMU), the Universiti of Brunei (UBD), and Sabah Parks worked to document and study the amphibian and reptile diversity at two focal locations Brunei Darussalam and the Malaysian state of Sabah. In Brunei, 16 students from JMU and UBD participated in a 3-week field course where they learned field sampling techniques, experimental design, and the challenges of conducting research in the field where so many variables are unpredictable. In Sabah, a small team of U.S. and Malaysian researchers worked to document the herpetofaunal diversity in Crocker Range National Park, an important, but poorly studied UNESCO's Man and the Biosphere (MAB) reserve site.
Figure 1. Sunlight streams through the mist in the mixed dipterocarp (large, broad-leafed tree) forests surrounding our research station. Photo by David S McLeod.
Figure 2. Hylarana erythraea. Students from James Madison University and the Univiersiti of Brunei had opportunity to become hands-on explorers around the Kuala Belalong Field Studies Center in Brunei. Photo by David S. McLeod
Figure 3. James Madison University graduate student, Sarah McGrath with Ahaetulla prasina (Oriental Vine Snake) in Crocker Range National Park, Sabah, Malaysian Borneo. Photo by David S. McLeod Figure 3. James Madison University graduate student, Sarah McGrath with Ahaetulla prasina (Oriental Vine Snake) in Crocker Range National Park, Sabah, Malaysian Borneo. Photo by David S. McLeod With the support of the Global Genome Initiative, a collection representing 40 genera and 81 different species was made and is now being DNA barcoded and studied. In addition to the specimens collected, notes on natural history, ecology, and behavior were recorded. Photographs were taken of nearly every specimen in life, documenting colors, textures, and the nuances of the living specimen that might be lost in preservation. Amphibians were swabbed to check for the presence of Batrachochytrium dendrobatidis, a fungus linked to amphibian die-offs around the globe, but not yet documented in northern Borneo. Tadpoles in the fast-flowing Bornean streams have evolved oral discs that allow them to “stick” to rocks in the current. This life stage of amphibians is poorly understood and the tadpoles of many species have not yet been described. Our project will use barcoding to match the DNA of adults with tadpoles in an effort to further our understanding of the natural history and evolution of amphibians. Figure 4. Tadpole underside. Photo by David S. McLeod
Figure 5. Sunrise over the canopy in the Heart of Borneo. The Kuala Belalong Field Studies Center, situated within Ulu Temburong National Park along the Sungai (River), is operated by the Universiti of Brunei as a site for research and education for both national and international students and researchers. Photo by David S. McLeod Borneo offered us amazing opportunities to observe, discover, and understand a small part of the island’s diversity! The fantastic herpetofauna included giant toads at the river edge with eyes that shone in our head lamps and frogs that communicate visually by waving their feet because they live around noisy waterfalls where calls alone are hard to hear. We also were fortunate to encounter Hornbills with their equally distinctive beaks and calls, and troops of long-tailed macaques moving gracefully through the trees along the rivers, and pairs of gibbons singing their duets to signify to the community that they are a couple. Borneo is truly a living laboratory. Borneo is paradise.
Figure 6. Training the next generation of biologists, ecologists, naturalists, systematists, and citizen scientists. Field courses such as the one in Brunei provide students from different backgrounds, cultures, and countries to come together as a community and foster the development of life-long partnerships across borders and boundaries. Photo by David S. McLeod
David McLeod holding Phrynoidis juxtasper. Photo by Sarah McGrath By David S. McLeod, edited by GGI Staff.
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Posted on 08/31/2016 in Collections, Global Genome Initiative, Research Expeditions, Vertebrate Zoology, Women in Science | Permalink | Comments (0) 08/17/2016
Revisiting the Tenasserim (Tanintharyi) of Myanmar The Global Genome Initiative (GGI) and the Smithsonian Myanmar Biodiversity Initiative are working with Fauna & Flora International's (FFI) on conservation research to protect and preserve Myanmar forests rich in biodiversity. The Tenasserim is an area on the Malaysian Peninsula that was politically contested between Myanmar and Thailand in the 1700’s; it later became an administrative unit under British-India and is now recognized as the Tanintharyi Region of Myanmar. The geography contains a mountain chain of lowland tropical forest and a coastal mangrove archipelago along the western edge.
Map showing the Tanintharyi Region of Myanmar; inset in lower right shows its location on the Malaysian Peninsula. The green area in the center map shows the region we visited in 2014, red in 2015, and red and blue areas were visited this year. Upper left image is a flying frog and lower left a venomous pit viper, and a bent-toed gecko above inset map, all observed on this year's expedition. Photos by Dan Mulcahy. This was my third summer in the Tenasserim conducting biodiversity surveys (see my blog from 2015); my focus is on amphibians and reptiles. One of the goals of FFI in Myanmar is focused in the southern Tanintharyi, to identify biodiversity values and the threats they face, with an emphasis on tiger conservation. With the tigers being a “top predator,” their fate is linked with that of the entire forest. Therefore, FFI has set up the Tanintharyi Conservation Program, working with the Myanmar government and non-governmental organizations in both Myanmar and neighboring Thailand to conserve the biodiversity in this region.
Zoology Lecturer Dr. Khin (center) and her students, Kyaw Yadanar Min (left) and Chuu Hay Mannre (right) from Myeik University, on a stream survey in the Tanintharyi Region, Myanmar. Photo by Dan Mulcahy The Smithsonian contributes through training and conducting research in biodiversity studies, by scientists with specialized taxonomic expertise. This year we worked with and trained students from the departments of Botany and Zoology, of Myeik University. Our surveys consist of hiking on trails and through streams, day and night, searching for amphibians and reptiles. The Zoology Department researchers worked with me, and two Myanmar conservation biologist colleagues Myint Kyaw Thura and Thaw Zin, studying the amphibians and reptiles of the Tanintharyi Region of Myanmar. The Tenasserim has a rich amphibian and reptile diversity that is important for taxonomic studies because it contains many "type localities" from early explorations (mid-1800's). A type locality is the place from where the specimens used to describe a new species were initially collected. This is important, for instance, when a widespread species is re-evaluated as multiple species. For example, the Black-striped Frog (Sylvirana nigrovitatta) was thought to range from India east to Vietnam, and China south to Malaysia. Now we are finding that it consists of multiple species based on genetic data. The type locality is "the valley of the Tenasserim River." Therefore, our genomic samples appear to represent the type material and will maintain the name Sylvirana nigrovitatta, while other more genetically (and geographically) distant populations will later be recognized as distinct species.
A juvenile Black-striped frog (Sylvirana nigrovitatta) perched on a moss-covered rock at the edge of a stream.
We have found up to four species of tree frogs in the genus Polypedates, a speciose genus common throughout Southeast Asia. This year we found many more, breeding on the trails and in bogs. They are "foam-nesters," meaning they lay their eggs in a nest of foam (on the ground or in vegetation), thereby keeping them moist throughout their development. This year we will use DNA Barcoding to verify which species lay their eggs on the ground, and which species lay their eggs in the vegetation, contributing to our knowledge of the biology and life history of this unique group of frogs. In summary, this year's trip to Myanmar was another success. We collected many genomic samples in order to fulfill GGI's goal to collect and preserve genomic biodiversity of life on Earth. We also trained students in biodiversity science and surveys, and I presented preliminary results of our amphibian and reptile DNA Barcoding work in the Tanintharyi at FFI's Tiger Conservation Workshop in Myeik. Our conservation research efforts in Myanmar are conducted under collaboration between FFI and Smithsonian Institution, funded through generous support of the Helmsley Charitable Trust, the European Union (Myanmar), and GGI. Each year I come back physically and mentally exhausted, thinking this will be the last trip I make—but once I recover, I can't wait to go back!
Dan Mulcahy presenting at the Tiger Conservation Workshop in Myeik. Photo by Myint Kyaw Thura. By Daniel Mulcahy (GGI) with comments by Melissa Songer (SCBI) and George Zug (NMNH), edited by GGI Staff.
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Posted on 08/17/2016 in Collections, Global Genome Initiative, Research Expeditions, Vertebrate Zoology, Women in Science | Permalink | Comments (0) 07/13/2016
Building Genomic Plant Collections from the Southeastern United States We, Drs. Carol Kelloff and Mark Strong, traveled to southeastern Virginia—resurveying botanical transects conducted over 70 years ago—to collect genomic material of plants for the Global Genome Initiative. The overall goal of our project is to build up the Smithsonian's Biorepository with genomic quality DNA samples and add herbarium vouchers of rare plants that will be available for study.
Mark Strong taking notes on habitat in the Blackwater Ecological Preserve, Zuni Pine Barrens. Photo by Carol L. Kelloff. The specific goal of our project is to collect plant species from Longleaf Pine ecosystems of southeast Virginia, collecting vouchers and providing valuable genomic tissue samples that can be used in future research. The availability of genomic tissue will facilitate phylogenetic studies of plant groups. It will not only provide more definitive species boundaries, but clarify the evolutionary relationships of plant groups. These results can be used by state, federal, or private agencies to provide evidence of the plants’ rarity and habitats in which they occur. This will improve efforts for habitat conservation, species preservation, and ultimately limit extinctions. We also intend to produce an annotated checklist of the flora in this ecosystem for the state of Virginia.
Longleaf Pine and Turkey Oak sandhills at the South Quay Sandhills Preserve. Photo by Mark T. Strong. It was amazing to walk the same sand roads through pinelands and pocosins (inland wetlands lacking flowing water) along the Blackwater River that Harvard professor Merritt L. Fernald did in the 1930’s and early 1940’s, when he collected plants for his work on the 8th edition of Asa Gray’s Manual of Botany. On this expedition, we focused our efforts on some of the rarest plants in Virginia found within the northernmost extent of the Longleaf Pine ecosystem. Many of these plants were initially discovered 70–80 years ago by the Harvard professor and his colleagues. Longleaf Pine communities, once a dominate ecosystem, now occupy less than a quarter of their original range. We were targeting the northernmost extent of this ecosystem (southeastern Virginia) to sample rare and endemic plants. Forty to sixty percent of species found in Longleaf Pine communities of the United States are estimated to be endemic, meaning they only occur this region and nowhere else on Earth—some of these are endangered or threatened. On this trip (late May), we were sampling the plants flowering in spring, and on a later trip in September, we will sample those that flower in summer and fall.
Nick Flanders, Toni Dotterer, and Peter Schafran (left to right). Photo by Carol L. Kelloff Arriving at the Blackwater Ecological Preserve, managed by Dr. Lytton Musselman of Old Dominion University (ODU), we met with Peter Schafran, a graduate student at ODU working on quillworts (Genus Isoetes), and two other students, Toni Dotterer and Nick Flanders. They are knowledgeable of where populations of many of the plants we are seeking can be found and have kindly offered to guide us around the preserve.
Pixie Moss peeking out beneath layer of pine needles (left) and Galax along bank of the Blackwater River (right). Photos by Mark T. Strong. We would like to highlight several of the more characteristic and rare species of these communities that we found. Species in two of the six genera of Diapensiaceae are represented here, Pyxidanthera barbulata (Common Pixie Moss) and Galax urceolata (Galax). The Pixie Moss is known only from pine barrens in five States, NY (Long Island), NJ, VA, NC, and SC while the Galax is more common, occurring in eight southeastern States. Another genus, Zenobia pulverulenta (Dusty Zenobia), in the Ericaceae, is known only from four States, VA, NC, SC, and GA.
Dusty Zenobia in full bloom, the branch turned upwards showing inside the petals. Flowers are borne in clusters along the branch and typically face down. Photo by Mark T. Strong. Our spring trip was very successful. We found 22 of our 24 target species that grow in the spring/early summer. In all, we collected 86 specimens from 42 families and took numerous photos of plants and their habitats. We also found immature populations of six other target species that we will collect material of later in September. The summer/fall growing season in these habitats is much more diverse, so we expect to double our numbers the next trip. By Carol Kelloff and Mark Strong (edited by GGI Staff) Credits/Acknowledgements: We thank Darren Loomis and Rebecca Wilson (Virginia Deparment of Conservation & Recreation) for granting us collecting permits and access to the Antioch, Blackwater, and South Quay preserves; Lytton Musselman (Old Dominion University) for granting us access to the Blackwater Ecological Preserve); and the Department of Botany, Smithsonian for their support.
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Posted on 07/13/2016 in Botany, Collections, Global Genome Initiative, Research, Research Expeditions, Science, Science and Technology, Women in Science | Permalink | Comments (0) 06/20/2016
An Interview with an Orchid Specialist. The Global Genome Initiative’s-Gardens team spent the cooler months of January, February, and March within the expansive, climate-controlled confines of the Smithsonian Gardens greenhouses in Suitland, Maryland. We worked primarily with facilities manager, Vickie DiBella; horticulturalist, Matthew Fleming; and orchid collection specialist, Tom Mirenda. Our goal was to collect as many genome-quality orchids for the Smithsonian’s biorepository and our efforts produced nearly 200 specimens.
Views inside Greenhouse 11, where orchid species are kept at Smithsonian Gardens in Suitland, MD. Photo credit: M. Gostel (left) and Smithsonian Gardens (right). On any given day, thousands of orchid specimens may be in bloom, displaying anything from a single, extravagant flower to something smaller and nondescript (to the human eye!), or perhaps even an elaborate hanging or stalked inflorescence (the term for the stem where a group or cluster of flowers are born on a plant). On our last day of collecting, we sat down with Tom to talk about this impressively diverse family of plants and specifically about the living collections stored in the Smithsonian Gardens’ greenhouses. This interview has been edited for length. GGI-Gardens: How did you first become interested in orchids? Tom: My interest began when I was eight or nine years old, actually. I used to browse through bulb and seed catalogs and order plants with my Christmas money. The first orchid I acquired was a Habenaria radiata that I grew from a tiny bulb—the egret flower. I would sometimes get in trouble with my mother when bulbs would arrive. My interest really took off when I moved to Hawai’i for college, though—they were so much easier to grow in the tropical climate there.
Assorted diversity of some representative orchid genera. (A) Paphiopedilum spiceranum (B) Phalaenopsis sp. hybrid (C) Psychopsis mariposa (D) Trichopilia sanguinolenta (E) Zygopetalum maculatum (F) Bulbophyllum compressum (G) B. echinolabium (H) B. flabellum-veneris (I) B. thiurum (J) Dendrobium thyrsiflorum (K) D. rigida (L) Angraecum sesquipedale. Photo credits M. Gostel (A, C, D, E, F, G, H, I, J, K) and Smithsonian Gardens (B). GGI-Gardens: What is your favorite thing about working with orchids? Tom: The sheer diversity of the plants—you can just never be bored working with them. There is always something new. This, combined with the artistry of horticulture and the patience required to grow something like this. I’m fascinated by the mystery of why flowers might look the way they do, how they engage in mimicry, deception, and manipulation of their pollinator partners. Some even manage to produce sex pheromones of would-be pollinating insects. The manipulation by orchids of pollinators, the evolutionary history and creativity that is reflected in it. I’ve been reading a lot of Richard Prum (an evolutionary biologist at Yale) who feels that aesthetics play a role in the evolutionary process. Diversity does not seem to be explained by selection alone—we see that in human intervention—resulting in the production of hybrids. GGI-Gardens: It’s really amazing, the diversity. Do you have any favorites in the orchid family? Tom: For me it’s the thing that’s flowering the best at the time! That and I suppose the genus Trichopilia, hummingbird pollinated Scaphyglottis, miniatures (Lepanthes for example), Trisetella hoeijeri, which has these remarkable flowers that are three times longer than its leaves, they just sparkle. Unfortunately I’ve never been able to get it to grow here. GGI-Gardens: Sounds beautiful. So when did the Smithsonian Gardens’ interest in orchid collections really begin? Tom: 1973, a committee was formed that included Mrs. Ripley as well as then horticulture director, Jim Buckler. It has continued to grow from there, through collections from all over the world, donations—one from the Pabst Blue Ribbon company—and another, more recently, from the estate of the late Dennis Roessiger, in Maine that included about 1,000 species! GGI-Gardens: Wow! How many total specimens would you estimate are in the collection now? Tom: Oh, we’re well into in the mid 8,000’s or 9,000s by now. GGI-Gardens: Do you have an estimate of the number of genera? Species? Tom: I’d guess about 250 genera and 2,500 species. GGI-Gardens: How do you envision the collection in the next 20 years? Tom: It’s always changing and growing. We’re doing some really neat things right now for example, one challenge here in the greater metropolitan DC area is the water quality. Some orchid groups are very sensitive, you have to be careful with chlorine and fluoride especially. We recently received a grant from the Smithsonian Institution’s collections program fund to collect and utilize rain water. GGI-Gardens: Interesting, not only a means to perhaps improve the quality of collections, but a sustainable approach as well. Along those lines, are there any ongoing conservation or preservation programs that are trying to protect the living collections at Smithsonian Gardens other than GGI-Gardens? Tom: For sure, the North American Orchid Conservation Center (NAOCC) is one. It includes orchids from all over North America. The Smithsonian is interested in taking this model global—if funds become available to do so—to assess the status of and determine priorities for species conservation and reintroductions. We sample populations and add them to a growing seed bank as well as a mycorrhizae bank. This is done at SERC (the Smithsonian Environmental Research Center). It’s extremely difficult work, being led by Dennis Whigham, Melissa McCormick, and Jay O’Neill. GGI-Gardens: Bringing these communities together is a big deal. How about the public? I’m sure they might be reading this blog article and wondering how they and other members of the Smithsonian community might be able to see the orchid collections throughout the year? Tom: We have native species planted at the National Museum of the American Indian that should be blooming in May and June. We always have display cases at the National Museum of American History, and also in the Castle building. Smithsonian Gardens has an exhibit called “Design for Small Spaces” running through August 31, 2016 that you will find in the Ripley Center Concourse. The Kogod courtyard at the National Portrait Gallery is another. Definitely keep an eye out for the 2017 Orchid Exhibit that will be in the Hirshhorn. We have a huge online database that is always available, with high quality images. Also, I write two articles each month for Orchid Magazine—these have all been archived and added to Encyclopedia of Life. GGI-Gardens: It sounds like opportunities are all over the area throughout the year, I look forward to checking them out! Thanks so much for your time. After our chat with Tom, we head into the greenhouses to resume collections. As we navigate the corridors of neatly arranged potted and hanging epiphytic (plants that grow on other plants) orchids in the greenhouses, clippers in hand, and ask to collect one or another specimen, we sometimes catch something like a protective reluctance in Tom’s answer: “I guess you can have a sample of this—I really love this plant. It’s not for display, but please be careful.” We always are careful and delicate when handling these living treasures and we’re not the least bit surprised by Tom’s reluctance. The nurture and patience required to maintain such an enormous collection is evident and who could not feel a protective, almost parental concern for them.
The GGI-Gardens team (from left to right): Morgan Gostel, Tom Mirenda, Kathryn Faulconer, Maryam Sedaghatpour, and Samantha Vo at the Smithsonian Gardens Greenhouse Facility in Suitland, Maryland.
By Morgan Gostel, GGI Buck Postdoctoral Fellow (edited by GGI staff).
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Posted on 06/20/2016 in Botany, Collections, Global Genome Initiative, Research, Science | Permalink | Comments (0) 05/27/2016
Surveying the Sumacs and Mosses of North America I am a Museum Specialist in the Department of Botany and the research assistant to curator Jun Wen, whose expertise includes grapes – the plant family Vitaceae, ginseng – the plant family Araliaceae, cherries – the family Rosaceae, and many plant groups found both in eastern Asian and North American that are biogeographically disjunct (species that are related, but separated geographically). Wen is a passionate biogeographer, an inveterate collector of plant specimens, and a strong believer in the collaborative process. Of all the tasks and projects I am given, an opportunity for fieldwork tops the list.
From Left to Right: Zhumei Ren, Sue Lutz and Joe Boggs (Ohio State University) collecting sumac galls in Liberty, Ohio in August 2015. Recently, I was able to participate in a GGI-funded collecting expedition to study the relationships and geographic patterns of sumacs and mosses in North America. For this particular trip we were joined by Dr. Zhumei Ren, a longtime colleague from China. Ren has been on several collecting trips with me in the past, but this was not our usual plant collecting trip. While we often collect plants that are disjunct species between North America and eastern Asia, we are not usually collecting a plant species that has a 48-million-year-old relationship with an aphid. But that is exactly what we set off to do. The aphid, Melaphis rhois, has co-evolved with two separate plant hosts integral to its life cycle. The primary host are sumac trees (Rhus); the aphid creates a sumac gall upon which it feeds. Galls are abnormal plant growths caused by the feeding or egg-laying activity of insects. The gall created by the Meaphis aphid is the summer home to a single female aphid where she reproduces for several months. The secondary hosts are the mosses growing in the area. As autumn approaches, the galls are slit open and the aphids fly to the moss beds where they reproduce again and overwinter. In the following spring, the larva feather and fly to the primary host for producing and mating. The mated female will produce a single female baby and the life cycle continues. Interestingly the sumac-gall aphids also show a disjunct distribution with the related aphid group, subtribe Melaphidina, distributed in eastern North America and eastern Asia.
Sumac galls on the leaves of Rhus glabra, collected in Newton Co., Georgia, August 2015. Our goal on this trip was to collect samples of the unique sumac species in North America over their geographic range in the eastern U.S. in order to conduct more extensive molecular analysis, particularly focusing on the phylogenetic diversity of the species and its disjunction. While these sumac trees are common, finding trees with sumac galls is a matter of chance. The galls are located on the undersides of the leaf, are globular, and vary in size with the largest about the size of a golf ball. They are often reddish in color, but can also be yellow to light green. We targeted locations that would encompass their geographic range from south to north, but we had a small window of time in which to collect them: when the aphids are mature, but before the galls are open. We needed to rely on first-person reporting to locate each site. We hit the lottery with Joe Boggs from the Ohio State Extension Service Office. His directions were precise and he met us on site to relate the history of this particular stand of Rhus/gall activity. Boggs departed for the extension office while we continued to collect plant, gall, and moss specimens. As we were packing up our gear Boggs returned. Because Rhus is a member of the Anacardiaceae family (poison ivies and oaks as well), he was concerned that we were exposed to the rash-causing oil, urushiol. He gave us a bottle of poison ivy scrub to remove the oils—good old Midwestern hospitality—and because of this he became the highlight of our trip.
Zhumei Ren & Jun Wen collecting sumac-gall aphids with graduate students in Wufeng, Hubei Province, China (September 2014). We continued south to Georgia, made a pit stop at the museum to offload specimens and replenish supplies, and continued north to New York, Vermont, and New Hampshire. It was a frantic road trip to make the collections within the prescribed time limit. We successfully collected in every targeted geographic area. But a road trip like this is not without its favorite moments. Our favorite saying on this trip came from our vehicle GPS guide, when we veered off the preset course – “Take a U-turn (big pause) if possible” – always sounding like it feared a liability. The collections made from North America will be studied along with many specimens already gathered in China by Zhumei Ren, Jun Wen, and their collaborators to unravel the biogeographic and evolutionary history of this unique group. By Zhumei Ren, Museum Specialist, Department of Botany (edited by GGI staff).
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Posted on 05/27/2016 in Botany, Collections, Global Genome Initiative, Research, Research Expeditions, Science, Women in Science | Permalink | Comments (0) 05/04/2016
Exploring the Flora and Fauna in the Horn of Africa A team of researchers from the Smithsonian Institution and USGS recently spent a month conducting biological surveys in Djibouti (pronounced ‘ji-BOO-tee’), a small country in the Horn of Africa. Djibouti is surrounded by Eritrea, Ethiopia and Somalia with coastlines that abut both the Red Sea and the Gulf of Aden. The country is approximately 23,000 sq. km and ranges in elevation from -155m below sea level to over 2,000 m; making this a potentially interesting place to conduct biodiversity surveys. This particular trip was the final expedition of a two-part project funded jointly by the U.S. Navy and the Global Genome Initiative (GGI) to survey the flora and fauna and provide the U.S. Navy with information that will be used to create a Natural Resource Management Plan and support the Bird Aircraft Strike Hazard (BASH). As the Principal Investigator of this project, I had the opportunity to work with mammologists, ornithologists, herpetologists, entomologists, and botanists to complete this task. We spent our days and nights preparing, documenting, observing and photographing as much of the flora and fauna as possible during the spring of 2014 and winter of 2016 with two goals in mind. Firstly, our aim was to help the U.S. military understand the biodiversity of wildlife on Camp Lemonnier (a military base located in the center of the country), and secondly, to provide species information to the Djiboutian Ministry of the Environment.
2016 Field camp crew at the Forêt du Day (Day Forest), Djibouti, including students from the local university and staff from the Center for Education and Research Department. Left to Right: Ali Dabelah, Ali Merito, Abdourahman Ismael, Mohammad Ahmed, Steve Gotte, Adwa Ali, Jim Whatton, Yahya Moumine, Brian Schmidt. (Seated): Adam Ferguson, Carla Dove, Kamil Mohamad, Molly McDonough, Jeremy Jacobs. (Photo: Camptment of Forêt du Day).
Prior to our expedition, Parker’s Pygmy Gecko (Tropiocolotes somalicus) was presumed to be rare because it was only known from a few museum specimens. It was the most common lizard we encountered in disturbed second growth habitat, indicating its presumed rarity is a product of the lack of surveys in its limited range rather than true scarcity. (Photo: S. Gotte) This information will ultimately aid the Djiboutian government in conservation efforts and in designation of critical habitat for protection measures. The specimens and genetic material we gathered will also act as a reference library of potential invasive species that could be unintentionally transported, allowing for faster identification and response to introductions of non-native species.
The Darkling Beetles, a family with more than 20,000 species known worldwide, are a dominant part of the insect fauna in desert regions, and the specialty group of study for Warren Steiner of the Smithsonian Department of Entomology. These flightless Adesmia were conspicuous and common on and around Camp Lemonnier, and active during the day. (Photo collage: W. Steiner) Our work took us to the nearby shoreline of the Gulf of Aden, to an off-site airfield, and into the rugged mountains of the ecologically unique Day Forest (Forêt du Day). As a result of the two expeditions we now have genetic samples for thousands of insects—now being tested for disease vectors and being used to help describe the insect life; more than 70 species of birds—some documenting new distributional records for the country and providing new resources for world collections; more than 14 mammal species including Speke’s Pectinator and Abyssinian Genet—rare species in museum collections; about 24 species of amphibians and reptiles including Dodson’s toads, Parkers Pygmy Geckos, and a Nubian Spitting Cobra, and several species of highly adaptive plants.
Collected by a variety of sampling techniques and traps, thousands of Djibouti insects and arachnids still await study by many specialists. Based on studies of target taxa so far, nearly all represent new additions to the Smithsonian collections. Ectoparasites were also collected from the many vertebrate specimens and may shed light on local disease vectors. (Photo collage: W. Steiner) During the most recent expedition to the Day Forest, we traveled for four hours to reach our destination north-east of Djibouti City. This forest is a very special place within Djibouti and only one of two high elevational (1,500 m) closed forests in the country. We stumbled across a large troop of Hamadryas baboons while searching for a glimpse of the endemic and critically endangered bird Djibouti Francolin (Pternistis ochropectus). We were fortunate to have special guests from the local university and the Djiboutian Center for Education and Research Department (CERD) join us in the Day Forest. Two students and two CERD employees eagerly participated in fieldwork activities by assisting the Smithsonian Team with observing the wildlife of the forest.
The Djibouti Francolin (Pternistis ochropectus) is endemic to the high-elevation mountains of Djibouti. This species is critically endangered and restricted to only two areas within the country. (Photo: C. Dove) Having DNA sequence available in on-line libraries will benefit science in many ways. Potential new species or species range extensions will be identified; genetic information will be available for researchers working in the region; bird DNA sequences will be available for the identification of bird/aircraft collisions in the region; U.S. Navy will have baseline ecological information as they move forward with development of Camp Lemonnier; and information regarding potential conservation of habitat and species diversity will be available to the government of Djibouti.
Rusty Russell (Dept. of Botany) with Apple of Sodom (Calotropis procera). This milkweed relative, originally described from a Middle East collection, extends into the Horn of Arica and throughout the Rift Valley. It can establish itself in the poorest of soils and its dramatic looking fruits are 90% air. Our trip was a big success, but more biological inventory work is needed in this country to document species diversity and improve knowledge for regional conservation planning. Hopefully, GGI and the Smithsonian will partner with the Djiboutian government for surveys in the future! By Dr. Carla Dove, Birds Program Manager, Vertebrate Zoology, NMNH (edited by GGI Staff).
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Posted on 05/04/2016 in Botany, Collections, Global Genome Initiative, Research, Research Expeditions, Science, Science and Technology, Vertebrate Zoology, Women in Science | Permalink | Comments (0) 03/30/2016
What's that Genome in the Sand? Wild animals that are directly visible in their environment are the main attraction for nature lovers. Most people do not know about the existence of a fascinating hidden world of animals that inhabit marine sand. This sand can host an impressive abundance and diversity of microscopic animals known as “meiofauna.” These meiofauna are not only a key part of life's food chain and fundamental to keeping sediment clean, but they can also be used to address important questions in evolutionary ecology. For instance, how and why are there so many diverse species on Earth? How do they evolve in relation to time and different ecological conditions? How do geographical and geological barriers affect gene flow among populations?
Collecting sediments for meiofauna along the coasts of Azuero Peninsula and Iguana Island, Panama. Photo by Ulf Jondelius These questions can potentially be answered by investigating the genomic diversity present in a small quantity of sand. Genotypes are correlated to the ecological conditions and geological histories of the environment. They can be used to infer the evolutionary origin of the group, and to infer how these organisms relate to each other; they are important to consider in existing general models of evolutionary ecology. Unfortunately, the genomes of meiofauna are poorly known. Our lack of knowledge is mostly because it is very difficult to identify these animals. It requires trained taxonomists spending several hours sitting at the microscope.
Some representative meiofauna. From upper left: an annelid, a nemertean, a gastrotrich, and the anterior part of a nematode. In the bottom, from left, a mollusk, platyhelminths Proseriata and Rhabdocoela, and a xenacoelomorph. Photos by: Freya Goetz (Annelida, Nemertea, Platyhelminthes), Ulf Jondelius (Xenacoelomorpha), Antonio Todaro (Gastrotricha), Alberto de Jesus Navarrete (Nematoda), Katharina Jörger (Mollusca). I am Francesca, a Buck Global Genome Initiative (GGI) fellow interested in investigating the genomes of meiofauna and how their levels of diversity change through time. I aim to compare the genomes of species that have been separated by known geological events, such as the raising of the Panama Isthmus, and identify genetic markers that reflect environmental changes. Working on very tiny animals, which also lack published genomes, is very tough. I spent part of my research learning genomics techniques and data analysis at Hubbard Center of Genome Studies at the University of New Hampshire, in Durham, under the guidance of Prof. W. Kelley Thomas and his staff. The collaboration among different research groups is always inspiring and exciting. Despite the challenges these organisms pose, we succeeded in retrieving the genomes of several species from the phyla Annelida, Nematoda, and Nemertea. Our preliminary and exciting results encouraged me to increase the number of species I will look at and the number of places I hope to find them, as well as to increase our knowledge about the genomic information of these microscopic organisms. With these goals in mind, I organized an international workshop in Panama by inviting several specialists from Europe, South and Central America, and the US to collect, identify, and preserve meiofauna.
Meiofauna workshop laboratory. We settled the laboratory, complete with our microscopes, at Achotines Bay, Azuero Peninsula. Here, we processed samples, investigated and digitized specimens, and fixed them for future genomics studies. Photo by Ulf Jondelius We focused on the still unexplored Pacific side of Panama, namely Azuero Peninsula and Iguana Island, sampling from 0 to 20 meters depth. The meiofauna laboratory was located at the Achotines Lab facility. About 2,000 specimens belonging to at least 10 phyla, tens of families, and hundreds of morphological species were collected. A digital image was made from each one, and they are now stored at the NMNH Biorepository with the aim to preserve and investigate their genomes. The workshop, funded by 2015 GGI Awards, was very successful in increasing the knowledge of this hidden and important ecosystem and preserving their genomes for future fundamental evolutionary ecological questions.
Participants of the meiofauna workshop, with a view of Achotines Bay in the background. From the left side: Maikon Di Domenico (Universidade Federal do Paraná, Brazil), Alberto de Jesus Navarrete (El Colegio de la Frontera Sur, Mexico), Ulf Jondelius (Swedish Museum of Natural History, Stockholm, Sweden), Antonio Todaro (University of Modena and Reggio Emilia, Italy), Tom Artois (Universiteit Hasselt, Belgium), Freya Goetz (Smithsonian National Museum of Natural History, Washington D.C.), Marco Curini-Galletti (University of Sassari, Italy), Francesca Leasi (Smithsonian National Museum of Natural History, Washington D.C.), and Katharina Jörger (Ludwig-Maximilians-University of Munich, Germany). Photo by Matthieu Leray By Francesca Leasi, Buck-GGI Postdoctoral Fellow, NMNH.
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Posted on 03/30/2016 in Collections, Global Genome Initiative, Invertebrate Zoology, Research, Research Expeditions, Science, Science and Technology, The Next Generation, Women in Science | Permalink | Comments (0) 03/16/2016
The resident bird gets the butterfly. When you look around you might notice birds going about their daily business. But what are they up to? It’s likely that they are foraging—looking for something to eat. Perhaps you’ve never thought much about what birds eat, but there’s a lot more to it than just worms, as the popular expression suggests. Many birds are insectivorous, meaning that they eat arthropods, a broader taxonomic group that includes insects and spiders (among other invertebrates). As part of a Smithsonian sponsored project, I am collaborating with Luke L. Powell and Peter P. Marra of the Migratory Bird Center, Robert C. Fleischer of the Center for Conservation and Evolutionary Genetics, and Delano S. Lewis at Northern Caribbean University in Mandeville, Jamaica, to investigate the diets of insectivorous birds, as well as the poorly known but amazingly diverse community of Jamaican arthropods.
American redstarts are migratory birds that travel to Jamaica during the winter and potentially compete with resident birds, like the Yellow Warbler, for food. Photo by Dave Inman. CC By-NC-ND 2.0
Andreanna Welch sifting through leaf litter in a Jamaican forest to collect ground-dwelling arthropods. Photo by Luke Powell. Our goal is to understand diet competition among resident Caribbean birds, and the millions of other birds that migrate to the Caribbean each winter. Specifically, we are studying two species, the yellow warbler (Setophaga petechia) and the American redstart (Setophaga ruticilla), at a long-term ecological research site at Font Hill Nature Preserve, Jamaica. In order to do this we are using cutting-edge, next-generation sequencing technology to sequence part of a gene (cytochrome oxidase I) of all arthropod diet items that have passed through the bird digestive tract and are excreted in their feces. We sequence all of the arthropods in the feces simultaneously, using a recently developed approach known as metabarcoding. We can then match the DNA sequences we obtain back to those of the arthropods living in the area, and figure out what the birds are actually eating.
Luke Powell using an aspirator to collect tiny beetles that have fallen onto a white shower curtain after vigorously shaking forest vegetation. Photo by Andreanna Welch The little that we know about Jamaican arthropods suggests that they are very diverse. For example, even though Jamaica is 1/10 the size of Cuba and 1/7 the size of Hispaniola, the island has 20 species of jumping spiders, 45 species of fireflies, 20 species of butterflies and 6 species of ants that are found nowhere else in the world. However, Jamaican arthropods in general have not been studied extensively, and there are very few DNA sequences available in online databases, such as the Barcode of Life database, to which we could match the diet item sequences.
Delano Lewis, a Jamaican entomologist, uses the sweep net to sample arthropods from higher up in the forest canopy. Photo by Luke Powell. The goal of our GGI funded project is to survey Jamaican arthropods in the Font Hill Nature Preserve to create a set of arthropod museum vouchers, collect genomic-quality samples, and obtain DNA barcode sequences for each species that we collect. This will be important for understanding the biodiversity of the arthropod community there, and providing a baseline for future studies on the impacts of humans and global climate change. The information and samples collected during our study will also be an important resource for entomologists examining the evolutionary relationships of arthropods in Jamaica and elsewhere in the world. Beyond all this, the DNA sequences we obtain will help us to gain a better understanding of how bird species with similar diets are able to co-exist during the winter, which is one of the most food-limited times of year. By Andreanna J. Welch, Research Associate at the Center for Conservation and Evolutionary Genetics in the Smithsonian Conservation Biology Institute (edited by GGI Staff).
Black-light trapping a diverse array of moths, beetles, and other species. Photo by Luke Powell.
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Posted on 03/16/2016 in Collections, Global Genome Initiative, Invertebrate Zoology, Research, Research Expeditions, Science, Vertebrate Zoology, Women in Science | Permalink | Comments (0) 03/03/2016
Cryptobiotic Condos—How Genomics Helps Monitor Coral Reefs The following is a blogpost about an expedition sponsored by the Smithsonian's Global Genome Initiative. There’s more to reefs than fishes and coral, far more. In fact, it is estimated fishes and coral make up less than 1% of all reef-associated animal species. The other 99% of reef diversity – what is known as the cryptobiota – live within the reef matrix and play a critical role in reef functioning. Not to be confused with yetis, bigfoot, or the Loch Ness Monster, crytopbiota are generally small, often tiny, and largely understudied. They contain members from across almost all branches of the tree of life. This hidden component lies among the nooks and crannies, and is what I aim to document as a research zoologist here at NMNH. One way to get at these cryptic communities is through the use of Autonomous Reef Monitoring Structures (ARMS). ARMS are constructed as standard units, consisting of a stack of 9 PVC plates that mimic the complexity of the reef. Like pre-fabricated homes, these units are deployed for a period of time, recovered and analyzed to see who has moved in. Because they are standardized, ARMS can be compared around the world and over time to measure patterns and changes in marine biodiversity.
ARMS have become the standard for reef biodiversity monitoring across the marine world, especially for marine community members that are hard to quantify. More than 1200 ARMS have been deployed at more than 100 sites worldwide, with the installations in Costa Rica being the first in the tropical Eastern Pacific. Map credit – Smithsonian Global ARMS Program. Recently, the Global Genome Initiative (GGI) provided funding for ARMS to be deployed at three sites in the Islas Murciélagos, in Sector Marino of the Area de Conservacion Guanacaste (ACG), off the Pacific Coast of northwestern Costa Rica. These are the first installations of ARMS in the tropical Eastern Pacific. GGI is a collaborative endeavor to collect the Earth’s genomic biodiversity, preserve it in the world’s biorepositories, and make it available to researchers everywhere. This project enables us to work strategically towards that goal by focusing on the collection, processing, and preservation of genomic material from poorly known – yet extremely diverse – communities.
A view from above the research station overlooking the Bay of Isla San Jose where three of the ARMS are deployed. Photo: Chris Meyer After a year, we will collect the deployed ARMS and bring them back to the lab to sample them for biodiversity. The ARMS plates are disassembled plate-by-plate and photographed for spatial analyses. Motile specimens are sorted through different sized sieves; those larger than 2 mm are further sorted into taxonomic groups, which are then processed as standard voucher-based specimens and DNA barcoded. Similarly, representative vouchers are sampled from sessile specimens to build a comparable reference library of species. Once vouchers are taken, the plates are scraped clean and the resulting material is homogenized in a blender and preserved for DNA analyses. These sessile communities, and smaller motile fractions (< 2 mm), are analyzed all together using an advanced “next-generation sequencing" method called metabarcoding to get diversity profiles from each fraction. A portion of the samples is processed right away, while others are stored in the NMNH's Biorepository for future genomic research.
ARMS: Freshly deployed (July 29, 2015), and three months later (October 21, 2015) Photos Chris Meyer and Frank Joyce One of the ARMS sites is near the local research station in the Bay of Isla San Jose, so it can be easily monitored as it accumulates species and can be shown easily to visitors and students at the station.
Smithsonian researchers Seabird McKeon and Michele Weber deploying ARMS. A curious octopus checks out the new digs. Photos: Chris Meyer During the ARMS recoveries, along with our Costa Rican colleagues, we will be training "parataxonomists" who are local individuals interested in biodiversity studies, but have little taxonomic expertise in many of the marine groups. We use the ARMS and resulting specimens for first-hand taxonomic training about the cryptobiotic community . We are teaching the parataxonomists how to deploy and recover ARMS, so they can address their own questions in the future.
ARMS Deployment Team: Left to right – bottom row: Christopher Valle, Maria Marta Chavarria Diaz, Minor Lara, Gilbert Ampie, Michele Weber, Anibal Lara, top row: Yelba Vega, Jaime Nivia-Ruiz, Keylor Lara, Ivannia Angulo, Eric Palola, Sea McKeon, Chris Meyer. Photo by Chris Meyer By Chris Meyer, Research Zoologist in the NMNH's Department of Invertebrate Zoology (edited by GGI Staff).
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Posted on 03/03/2016 in Collections, Education, Global Genome Initiative, Invertebrate Zoology, Research, Research Expeditions, Science, Science and Technology, Women in Science | Permalink | Comments (0) 02/02/2016
Where Does Your Seafood Come From? Providing the world’s growing population with a sustainable and secure supply of seafood is a daunting task. Illegal, unreported, and unregulated (IUU) fishing is one of the biggest threats to global fisheries. IUU fishing in the Caribbean accounts for a large proportion of the spiny lobster and queen conch fisheries, which are the two most economically important in the region.
Caribbean spiny lobster (top) and queen conch (bottom). Photo By Nathan Truelove. For my postdoctoral research, under the supervision of Dr. Stephen J. Box, I am developing DNA-based traceability tools to help combat IUU fishing. This research project, supported by the Smithsonian Institute for Biodiversity Genomics and Global Genome Initiative, lead to me to Pedro Bank, Jamaica, which is one of several IUU fishing hotspots in Caribbean. My goal on this trip was to collect samples of Caribbean spiny lobster and queen conch in this region to start building a reference DNA-based database that will help us identify and track illegal fishing in the future.
Many artisanal fishers use Antillean Z-traps (left) to catch fish (right) and Caribbean spiny lobster. Pedro Bank is located 60 nautical miles southwest of Kingston, Jamaica and is the Caribbean's main fishing ground for spiny lobster and queen conch in this area. Almost all the spiny lobster harvested in Pedro Bank is consumed in the United States, while most of the queen conch is exported to the French Caribbean territories of Guadeloupe and Martinique. The lobster and conch fisheries in Jamaica generate several million US dollars per year and provides a crucial source of employment for artisanal fishers (fishermen and fisherwomen) living in remote coastal communities.
Not all of Pedro Bank is open for fishing. The Southwest Cayfish Sanctuary, located in Pedro Bank, is Jamaica’s first offshore marine protected area (areas protected for conservation purposes, like Bird Cay – the uninhabited seabird sanctuary). Pedro Bank has three small sandy cays located on the southwestern edge of the bank. Fishers inhabit two of the cays and the third, Bird Cay, is an uninhabited seabird sanctuary where fishing is not allowed. Middle Cay is home to approximately 500 artisanal fishers who spend up to 11 months a year on the cay. Though the Jamaican Defense Force Coast Guard conducts routine patrols of the waters of Pedro Bank to catch lobster and conch poachers, still up to one third of all the lobster and conch harvested in Pedro Bank are illegally poached by foreign commercial fishing boats then exported with a false origin of catch to cover their tracks. With the samples I collected, I am now at Stanford’s Hopkins Marine Station where I’m collaborating with Dr. Stephen Palumbi’s lab to develop DNA-based traceability tools for spiny lobster and queen conch, with the hopes of helping regulate and prevent illegal harvesting of these key commercial species in the Caribbean.
We discussed our research with artisanal fishers on Pedro Bank, who helped Dr. Courtney Cox and I collect genetic samples for our research.
Jaedon Lawe (moving from right to left) and Llewellyn Meggs, who are the founders of the Yardie Environmental Conservationists Ltd., helped Dr. Courtney Cox (Postdoctoral Fellow at the Smithsonian Laboratories of Analytical Biology) and I (far left) collect genetic samples of lobster and conch from Pedro Bank. The white dome shaped building in the background is the Pedro Bank Research Station. By Nathan Truelove, Postdoctoral Fellow at the Smithsonian Marine Station at Fort Pierce (edited by GGI Staff).
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Posted on 02/02/2016 in Collections, Global Genome Initiative, Invertebrate Zoology, Research Expeditions | Permalink | Comments (0)
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