National Museum of Natural History Unearthed

Preserving and Understanding the Genomic Diversity of Life on Earth

An introduction to the Global Genome Initiative from its Director, Jonathan A. Coddington.

Director Jonathan A. Coddington looking at spiders under a microscope in the Highlands Biological Station in southern North Carolina. Image by Taina Litwak, USDA.

Preserving and Understanding the Genomic Diversity of Life on Earth. This is a monumental mission statement. Some might even say impossible. But we here at the Global Genome Initiative (GGI) believe that there has never been a better time to undertake an enterprise of this magnitude.

The Global Genome Initiative, a component of the Smithsonian Institute for Biodiversity Genomics, is sending scientists and research teams to all corners of globe with a very specific mission: to collect, sequence, preserve, understand, and share the molecular makeup of every species on Earth. While GGI is housed at the Smithsonian, we are a growing collaboration among institutions from around the globe that share GGI goals.

African Dwarf Kingfisher (Ceyx lecontei). Image by Brian K. Schmidt, from field research in Gabon.

The genome is an organism’s instruction manual, the complete set of DNA and all of its genes. By exploring and preserving genomic material, scientists will be able to unravel the mysteries of the world around us. Extinction continues to threaten species all around the globe, often before we even know they exist, genomics research allows us to find, protect, and preserve these species. We have so much to learn from this research:

What are the basic kinds of organisms with which we share this planet?

How do organisms adapt to changes in their environment, and how can we use genomics to measure and respond effectively to environmental change?

Can we develop technologies to make identification of organisms more accessible to more people?

Answering questions like these can spur innovation in agriculture, help with the development of new medicines, and guide us down the path of sustainability and cutting edge technological advancement in nearly every facet of our lives.

Dan Mulcahy processing genomic samples for DNA sequencing in the NMNH lab. Image by Adrian Van Allen, Smithsonian Institution.

We like to think big, and we believe that GGI is laying a foundation for a new and exciting era of scientific research. As our research teams return from the field, and as exciting news in biodiversity genomics breaks, we will be sharing stories, pictures, and video with you, in the hopes that viewers can follow along with our expeditions, and discover the importance of this research.   

Follow along with the hashtag #SmithsonianGGI to join the conversation!

Rediscovering the Pangolin

It could be a Pokémon.  It could be a dragon’s egg.  It could even be a Transformer.  

Pangolin comes from ‘peng-guling,’ the Malay word for roller – the action a pangolin takes in self-defense. Ground Pangolin (Manis temminckii) at the Madikwe Game Reserve, South Africa. Image by: Masteraah, via EOL.

But actually, this is a pangolin. It’s not surprising that the pangolin looks so bizarre to us; its biology is unique even among other species in the natural world. In fact, scientists listed it as the sole species in the order of Pholidota, a grouping within scientific taxonomy used to classify organisms. The only Pholidotes in existence today are the eight species of pangolin, a tiny number when compared to other orders like Carnivora, which has more than 270 species. Within the pangolin family there are those that live in trees, and those who inhabit the ground and underbrush, both found throughout Africa and Southeast Asia in habitats ranging from savannas to rainforests.

Chinese pangolin (Manis pentadactyla) on view on the Kenneth E. Behring Family Hall of Mammals.

Having no teeth, these creatures live off of termites and ants. They use their long, sticky tongues to catch insects and two stomach chambers that aid digestion when they swallow insects whole. The pangolin has one of the longest tongues proportional to its size of any mammal. The Giant Pangolin’s tongue measures in at an impressive 27.5 inches! Unlike humans, a pangolin’s tongue is anchored to its sternum, a bone found in the chest area. In pangolins, the sternum has an extremely long, modified posterior section called the xiphoid process, which actually attaches muscles all the way down the abdomen wall and curves back behind the internal organs near the pelvis. This positioning greatly limits the pangolin’s ability to vocalize.

Instead of communicating through sound, pangolins use their incredible sense of smell to send signals to one another by excreting unique scents to mark their territory.  Pangolins are solitary and nocturnal creatures that roam the jungles, savannas and forests like vigilante exterminators, eating ants and marking their territory by leaving odors that warn other pangolins to stay away. Or, if it’s mating season, to come hither.  

Megan Krol, a collections technician at the National Museum of Natural History, finds a pangolin scale in the mammal collections. Pangolins are the only mammals known to possess a nail outside of their digits. It was previously thought that the scales might be modified hairs, which is why this scale is in a box with porcupine quills for a teaching collection. Image by P. Rylander, Smithsonian Institution.

You will never see pangolins swapping jokes at the local watering hole; they are so solitary that when forced together for long periods of time, pangolins can develop ulcers from stress. Male pangolins have even been known to fight to the death when forced together in captivity.  That is not to say that pangolins cannot coexist peacefully; pangolin mothers carry their young around on their tails until the next baby is born, typically giving birth around once a year.  

A pangolin carries its baby at a Bali zoo, Indonesia, June 19, 2014. Image by Firdia Lisnawati, AP Photo.

The most striking characteristic of the pangolin is its scales; they’re literally as tough as nails. Their scales are made of keratin - the same material found in human nails, which protects them from some pretty fierce predators. Pangolins are born with the same number of scales that they have all of their life, which harden rapidly as they grow older.  When the pangolin feels threatened, it curls into a tight ball like a ‘roly poly’ pillbug, using its incredibly strong tail muscles to completely cover its unscaled underbelly for long periods of time. This position makes it virtually impossible for lions or wild dogs to sink their teeth into a pangolin ball. 

However well protected these bundles of toenails may be to their natural predators, pangolins are helpless against humans and are the world's most trafficked mammal. An estimated 40,000-81,250 pangolins were collected in 2013 alone, but it could be more- since wildlife traffickers don’t exactly submit their numbers. While conservation efforts and international laws are being enacted to protect the pangolin, their biggest predators are poachers. In China and parts of Southeast Asia, the pangolin is considered a medicinal cure for a variety of ailments, including cancer, though this claim is completely groundless. In some parts of Africa, pangolins are seen as a good omen and are believed to bring good luck to those who eat them. Additionally, clear-cutting forested areas for agricultural purposes destroys termite mounds and tree based ants that pangolins rely on for nourishment and survival. 

To date, two pangolin species are classified as Critically Endangered and all species are protected under National and International laws. Poaching, in conjunction with habitat destruction, is rapidly affecting the pangolin population.  Soon, the creature you never knew existed may very well not exist at all.  

Help raise awareness about how wonderful and unique pangolins are, and educate those around you with facts about this species. Continue to learn about conservation efforts against the illegal trade of pangolins and other animals; it’s not too late to help save endangered species!

Indian Pangolin (Manis crassicaudata). National Park, Bharatpur, Rajasthan, India. Image by Ansar Khan Keoladeo, NBP Windland Smith Rice International Awards 2013.

 

By Paige Rylander, Public Affairs Intern, National Museum of Natural History

With specials thanks to Megan Krol, Collections Technician, National Museum of Natural History

Not Gone Yet, Some of Our Favorite Endangered Species

To raise awareness of Endangered Species Day, we spoke with our scientists to find out about species that are particularly meaningful to them. Which endangered species do you care about? Share your stories in the comments below!

Echinacea laevigata. Image by M. Peters.

Smooth Coneflower (Echinacea laevigata)  

By Melinda Peters, Collections Management, Botany

The cheerful face of the Smooth Coneflower is delightful for many reasons, but since 1992 it has been on the list of Federally Endangered Species. I decided to study the genetics of this plant in graduate school in hopes of helping conservation efforts. Currently this species is only known in VA, NC, SC, and GA. E. laevigata is a prairie plant, but due to the changing landscapes of America's prairie habitats, scientists have seen a decrease in populations because of habitat loss. Without grazers and natural fires on the land to maintain increasing encroachment of invasives and forest species, the prairie plants lose out and we see new communities forming. As these prairie plants become more segregated, it is harder for pollinators to find them and help distribute pollen for an increased genetic diversity. Funny enough, the largest populations of E. laevigata are in huge power line rights-of-way. They persist because the landscape is mowed, which mimics the act of grazing and in turn allows the populations to continue to flourish. These plants are important for the balance of these communities, which is why scientists are researching ways to conserve them. This is when I break into song and sing, “The Circle of Life.” Enjoy nature, and appreciate its beauty, but leave things in their place because they play a role in their community just like us. It is always a good idea to “stop and smell the flowers”- just do not pick them! 

 

Delhi Sands Flower-Loving Fly. Image by Marjory Nelson via U.S. Fish & Wildlife Service.

Delhi Sands Flower-Loving Fly (Rhaphiomidas terminatus abdominalis)

Erin Kolski, Museum Technician, Entomology

There is only one fly on the U.S. Endangered Species List: the Delhi Sands flower-loving fly. This subspecies of mydas fly is native to the Delhi Sands, a unique dunes habitat in southern California. The sands once covered about 40 square miles in Riverside and San Bernardino Counties, but urban development and agricultural expansion have reduced the habitat to isolated pockets a tiny fraction of their original size. The destruction of the Delhi Sands has led to the dwindling of the Delhi Sands flower-loving fly, along with other plant and animal species that can only be found in this unique habitat. While these flies and other endangered insects do not get the attention that the larger, more charismatic vertebrates do, they play a vital and often underappreciated role in ecosystems and deserve protection too!

 

A rosewood at the State Park of Rio Preto, Brazil. Image by M. Vatanparst.

Rosewoods (Dalbergia)

Mohammad Vatanparast, Postdoctoral Fellow, Botany

I found rosewood trees (species in the genus Dalbergia L.f.) to be important elements of our biodiversity when I started my studies on these species five years ago. They produce fine timbers of high economic value and many species of rosewood demonstrate nitrogen fixation by root nodules associated with bacteria. These species grow in diverse climate conditions in tropical and sub-tropical regions. More than 50 species are listed in the IUCN Red List as vulnerable or endangered mostly because of deforestation and logging. Conserving these precious species is one of my research goals and I hope that we can find a solution!

 

Sporagra (Carduelis) cucullata. Image by Siskini via Wikimedia Commons.

Red Siskin (Sporagra (Carduelis) cucullata) 

Brian J. Coyle, Postdoctoral Researcher, Vertebrate Zoology

The Red Siskin is an iconic and beautiful bird that once roamed the skies of northern Venezuela in large flocks. Such captivating displays like this first inspired my love and respect for the natural world, eventually leading to a deeper fascination with the tremendous diversity, complexity and history of life that surrounds us in almost any location on this planet. Unfortunately, decades of wildlife trafficking for the pet trade have decimated the Red Siskin population in Venezuela, where the species is now listed as critically endangered. Like many others, I feel an urgency to protect our remaining natural resources for future generations so that they too may be inspired to embrace sustainability. At the Smithsonian, I am contributing most directly to this mission through my participation in the Red Siskin Initiative. Scientists and experts from across the institution are collaborating with international partners to recover sustainable populations of Red Siskins in Venezuela through research, captive breeding, reintroduction, education and efforts to combat wildlife trafficking. Our team is also working to protect a previously undocumented population of this species that was discovered in Guyana in 2000 during a joint expedition between the National Museum of Natural History and the University of Kansas. I look forward to the day when large flocks of this highly endangered bird are again a common sight and the scourge of wildlife trafficking is greatly reduced.

 

The Flora of the Hawaiian Islands website has images for many species, including Argyroxiphium sandwicense subsp. macrocephalum from Hawaii’s Haleakala National Park. Image by Warren L. Wagner (L). Flowers of Argyroxiphium sandwicense subsp. sandwicense from Hawaii’s Maua Kea. Image by Bruce Baldwin (R).

Haleakalā Silversword (Argyroxiphium sandwicense)

Gary Krupnick, Head of the Plant Conservation Unit, Botany

For our 10^th wedding anniversary, we were fortunate enough to visit the island of Maui, Hawaii. We spent one morning hiking in the Haleakalā National Park. When we reached the rim of the dormant volcano, the view took my breath away. The amazing site before our eyes looked like a surreal painting, and scattered throughout this painting were spots of brilliant silver. On closer examination, those silver spots were plants called the Haleakalā silversword, also known as Argyroxiphium sandwicense subsp. macrocephalum. Endemic to Hawaii, these silverswords are listed as threatened by the U.S. Fish & Wildlife Service and as vulnerable on the IUCN Red List. Threats to this species' survival include introduced sheep and goats, loss of pollinators, and over-collecting. With proper protection, this subspecies is recovering nicely and it is now considered a successful conservation story. Unfortunately, the same cannot be said for its sister subspecies, the Mauna Kea silversword Argyroxiphium sandwicense subsp. sandwicense. This species grows on the big island of Hawaii, where only around 40 naturally occurring plants remain.

  

BHL Supports Science and Conservation

Museum specimens and records in historic literature and archives represent the only available information for many rare, extinct, and endangered species. In order to properly evaluate, study, and protect endangered populations, scientists require access to these records and specimens. The Biodiversity Heritage Library (BHL) is an open access digital library committed to providing free, global access to books and archives about the world’s plants and animals. With over 46 million pages spanning the past five centuries of recorded knowledge about Earth’s biodiversity, BHL includes a wealth of knowledge about endangered species and supports the work of scientists and conservationists around the globe.

I've worked with the Biodiversity Heritage Library in various roles since 2008, and what I love most about my job is that I feel like I'm making a true difference to the work of those committed to describing, understanding, and protecting our precious biodiversity. Historic literature and archival field books provide information such as species data, ecosystem profiles, distribution maps, inter-dependency observations, geological and climatic records, and an historical perspective on species abundance, habitat alteration, and human exploration, culture and discovery. This information has a multitude of applications in modern-day science. It is used to populate species databases and datasets that inform present-day research. It not only allows scientists to study biodiversity, but also to save it by enabling new species identification and facilitating the development of holistic conservation methods that integrate all of the factors necessary for a species’ wellbeing into its overall protection strategy. 

My work on the Biodiversity Heritage Library is helping scientists obtain free, open access to information that is critical to the conservation of not only endangered species, but life on our planet as a whole. As BHL's Outreach and Communication Manager, I spend most of my time sharing the awesome resources in our library via social media and working to ensure that as many people as possible know about the incredible free resources available at their fingertips. One thing I love to do in our social posts is highlight various species and books found in our collection, and to honor Endangered Species Day, I've selected a few of my favorite endangered species and shared information and beautiful illustrations from BHL below. 

 

Arakan Forest Turtle (Heosemys depressa). Anderson, John. Anatomical and zoological researches: comprising an account of the zoological results of the two expeditions to western Yunnan in 1868 and 1875. v. 2 (1878). Yunnan Expeditions, Plate LV. Digitized by Smithsonian Libraries.

Species One: Arakan Forest Turtle (Heosemys depressa)

In 2009, scientists saw one of the rarest turtles in the world for the first time in the wild. Believed extinct since 1908 until conservationists re-discovered it in a Chinese food market in 1994, the Arakan Forest Turtle (Heosemys depressa) was known to science by only a few museum and captive specimens until the Wildlife Conservation Society (WCS) team discovered five turtles in an elephant wildlife sanctuary in Myanmar in Southeast Asia. Listed as critically-endangered by the IUCN, the WCS team believes the elephant sanctuary holds promise as a focus for future conservation efforts for the turtle. 

 

The kākāpō (Strigops habroptilus). Buller, Walter Lawry. A history of the birds of New Zealand. (1873). Digitized by Natural History Museum Library, London.

Species Two: The kākāpō (Strigops habroptilus)

The kākāpō has many impressive distinctions. It is the world’s heaviest parrot. It is also the world’s only flightless parrot. It is found only in New Zealand, and, with a lifespan of up to about 120 years, it may be one of the world’s longest-living birds. Today, the total known population is less than 150 individuals. Human development and introduced predators decimated the kākāpō population, particularly in the 19^th century. Today, the Kākāpō Recovery Plan, implemented in the 1980s, monitors and protects the remaining population on three islands – Codfish Island (Whenua Hou), Little Barrier Island (Hauturu) and Anchor Island. 

 

Javan Rhinoceros (Rhinoceros sondaicus). Wolf, J. Proceedings of the Zoological Society of London. (1874). Pl. XXVIII. Digitized by Natural History Museum Library, London.

Species Three: Javan Rhinoceros (Rhinoceros sondaicus)

The Javan rhinoceros is probably the rarest large mammal in the world, with no more than 50 individuals left in the wild and none in captivity. The second-largest animal in Indonesia after the Asian elephant, adults are reported to weigh anywhere from 900-2,300 kg. Of three known subspecies, including the Indonesian Sunda rhinoceros, Vietnamese Sunda rhinoceros, and the Indian Sunda rhinoceros, only one – the Indonesian subspecies – still remains. While the Indian subspecies is believed to have gone extinct before 1925, the last remaining Vietnamese Sunda rhinoceros was killed by a poacher in 2010. Poaching, habitat loss, and lack of genetic diversity are the greatest threats to this species. Learn more about the rhinoceros and current conservation efforts from WWF.

 

You can find more amazing historic illustrations of endangered species in our Flickr collection and learn more on our blog about how BHL is helping to save biodiversity.

Guest post by Grace Costantino, Outreach and Communication Manager, Biodiversity Heritage Library