Tuesday, December 8, 2020

LAWRENCE — Antarctica, mostly covered in snow and ice, isn’t the first place most people might think to search for vital evidence about the evolution of plants. But Antarctica wasn’t always devoid of greenery. During the late Cretaceous, between 66 to 100 million years ago, parts of Antarctica looked more like a temperate rainforest.

For a paleobotanist like Brian Atkinson, assistant professor of ecology & evolutionary biology at the University of Kansas and curator at KU’s Biodiversity Institute and Natural History Museum, Antarctica today is a treasure house of plant fossils offering one-of-a-kind insight into how modern plants evolved and relate to each other on an evolutionary tree.

Recently, Atkinson earned a three-year, $850,000 grant from the National Science Foundation to lead a team from KU and the University of Michigan to collect and analyze fossilized flowering plants from promising field sites like the James Ross Basin and Vega Islands at the northern tip of the Antarctic Peninsula. Atkinson’s co-principal investigator is Selena Smith of the University of Michigan.

“My research group and I are interested in understanding the role of Antarctica in the early evolution of flowering plants,” Atkinson said. “The idea that Antarctica was an important area for the diversification or evolution of flowering plants in the Southern Hemisphere dates all the way back to the work of Charles Darwin, the 19th century naturalist.”

Because at one time Antarctica was at the heart of Gondwana, the southern supercontinent comprising Antarctica, South America, Australia, Africa, India and New Zealand, plant fossils from Antarctica can show how plants from these now-separated locales might be related. 

“Antarctica seemed to be at the center of it all,” Atkinson said. “My group is interested in going down to Antarctica and collecting exceptionally preserved flowering plant fruits, flowers and seeds — which we know from preliminary data are there — then describing those fossils and putting them into an evolutionary-in-biogeographic context. We’re also interested in understanding links between Antarctica and South America, as well as North America, because there’s some evidence from vertebrates that there was a biotic exchange between those three continents between 66 to 100 million years ago. My colleague Ari Iglesias at the Universidad Nacional del Comahue in Argentina has collected preliminary data.”

Atkinson said filling in gaps in the fossil record of flowering plants — which include everything from grasses to roses, cactuses and magnolia trees — would help scientists better understand a linchpin of our ecology, economy and society.

“Flowering plants comprise about 90% of terrestrial plant diversity that we see today —90% of plant species that we recognize are flowering plants,” he said. “Our livelihoods essentially depend on flowering plants. From what we eat to the clothes we wear to what we make our houses from, the vast majority of our economy can be related to plants. Even our culture is impacted by flowering plants. They’re the most diverse group of land plants that we see today with about 300,000 species, give or take a couple thousand.”

Atkinson’s work in Antarctica also could help paleobotanists better predict how the lion’s share of plant life on Earth will react to runaway climate change now underway all over the planet.

“Of course, the world is warming catastrophically, and these fossils can provide a paleontological forecast system, if that’s not too much of an oxymoron,” he said.

In Antarctica, Atkinson and his team will travel by ship to two islands in the James Ross Basin. There, they’ll set up camp and hunt for Cretaceous plant fossils, which sometimes appear as impressions of leaves and stems in exposed rock.

“Rocks are jutting over the glaciers, ice and snow pack,” he said. “We look for little dark potentially shiny reflective chunks in the rock. Sometimes it takes a few passes — but once you’ve found one plant fossil you find that same layer is more is likely to contain other fossil plants. The preservation is really good there for Southern Hemisphere plants, and overall western Antarctica has the age of fossils and types of fossils that are hard to find in many other places in the Southern Hemisphere.”

Once fossil specimens are collected, the team will bring them back to the U.S., and Atkinson will perform phylogenetic, comparative and biogeographic analyses to determine relationships between fossil species. Much of the analysis is possible because specimens from Antarctica are so well-preserved (down to the cellular level).

“This type of preservation is called permineralization,” Atkinson said. “I specialize in these type of fossil plants because they’re super well-preserved and you can find them throughout the geological record. It’s just that very few people have the expertise to study them. We know that including these fossils into evolutionary analyses can make really important impacts as far as inferring evolutionary patterns and relationships.”

Part of the work also will involve visits to institutions to visit for comparative material such as Kew Royal Botanical Gardens, Missouri Botanical Gardens, Smithsonian Museum of Natural History and Universidad Nacional de La Plata in Argentina.

Additionally, postdoctoral researchers, graduate students and undergraduates at both KU and Michigan will gain research training as part of the new award.

“The biggest training component will be for the graduate students,” Atkinson said. “My co-PI and I will recruit Ph.D.s, and it should be a synergistic endeavor in which these students will go down to Antarctica and learn a lot about Antarctic research and how to do fieldwork there. After the fossils are collected and returned to the U.S., they’ll learn how to curate, prepare and manage specimens. A lot of hands-on preparation techniques will be done here at KU, and fossils that are identified as suitable for CT scanning will be sent to Michigan, and the Ph.D.s will learn about CT scans and so forth.  We’re hoping the students can learn from one another by visiting each lab and then get really well-rounded traditional preparation techniques and more modern imaging techniques — that combination of skills is relatively uncommon. They’ll hopefully come out of this training as very well-rounded in specimen-based research.”

The researchers expect to begin fieldwork in early 2022.

Wednesday, December 16, 2020

LAWRENCE — When you imagine a visit to a natural history museum, the first thing that springs to mind could be dinosaur bones or taxidermized animals.

Behind the visitor displays, however, advanced research on specimens collected from around the world is taking place. What’s more, this work forms an essential front line of defense in pandemic preparedness.

According to Jocelyn Colella, research affiliate with the University of Kansas Biodiversity Institute and incoming assistant curator of mammals with the KU Natural History Museum, museums act as a kind of decentralized pathogen surveillance network. In a recent piece published in Science, Colella and colleagues argue that expanded biodiversity infrastructure will be an essential front line of defense in pandemic preparedness in the wake of COVID-19.

“Museum visitors see specimens on display, but hundreds and thousands of others are safely preserved behind the scenes — museum curators are responsible for making sure that those specimens are preserved and available for research going into the future,” she said. “Fifty years ago, we weren’t sequencing DNA. But now we are — and specimens preserved over decades, or even centuries, can now be used for molecular research. We have a couple of liquid nitrogen dewars here at the Biodiversity Institute that hold frozen tissues from all sorts of animals, from all over the world. Those tissues can be used to sequence whole genomes to identify how animals are adapting or responding to changing conditions.”

Colella said such collections preserve specimens and also capture the community of microorganisms that use the organism as a host.

“You can also sequence viruses, bacteria and fungi from all of those frozen tissues — so you not only get information on the host organism or mammal, but you also get information about their entire community,” she said.

Because more than half of all emerging diseases in humans come from wildlife, such as COVID-19 (which scientists think jumped to humans from horseshoe bats), museum specimens hold the genetic clues needed to determine where they came from and better understand and fight these pathogens — especially in countries at high risk for emerging zoonotic disease, such as those with high species diversity and a high frequency of human-wildlife contact.

“As the human population grows, we continue to come into contact with new, different and more animals. That increases the risk of these disease spillover events,” Colella said. “The cool thing with natural history museum collections is that we have sampling through time. You can survey the same areas over and over, sampling all sorts of different animals, which gives us a sense of how long a virus has been there and where it came from.”

The KU researcher pointed to hantavirus as an example where biodiversity collections collaborated with the Centers for Disease Control to help fight off a disease that had entered the human population from animals.

“Parallel to the current COVID-19 pandemic, there was a spillover event in 1993 of hantavirus in the American Southwest that led to the deaths of many people, and we had no idea where it came from,” Colella said. “The CDC asked the Museum of Southwestern Biology to help find the reservoir host of the virus, and they identified deer mice as the source. Researchers were then able to go back into these historic mammal collections and found that this disease had been in rodent populations for over 10 years before it spilled over into humans. That type of information allows us to have an evolutionary perspective on what happened between when this virus emerged in rodents and when it became harmful to humans — what changed? That allows us to respond and prevent outbreaks in the future.”

While the importance of natural history museums to human health has never been higher, in recent years the number of specimens being deposited in biodiversity collections actually has been declining.

A second paper written by Colella and colleagues, just published in BioScience, outlines ways to reverse this downward trend.

“Another reason scientists are having trouble identifying reservoir hosts and finding novel viruses is because the sampling base in museums just isn’t there, and it’s not because scientists aren’t taking samples,” she said. “It’s because there are no requirements for samples to land at museums or public institutions. There’s an ethical issue with collecting animals and then keeping all those samples in your personal freezer forever until you retire or lose all the IDs and can’t associate the material with XYZ, and it was all for naught. We can do better.”

According to Colella, several studies have tracked the number of deposited specimens across the past few decades and show “dramatic declines” starting in the late 1990s. “There are plenty of permits out there and specimens being sampled. The samples are just not ending up in museums,” she said.

The KU researcher and her co-authors propose treating specimens collected in the field exactly like other types of scientific data and using the open-data model to ensure scientists have access to museum specimens for research today and into the future.

“We propose increased open-data requirements by journals, integration of specimens into existing requirements for data management plans and a cultural shift in biological sciences. That must be collectively propelled by researchers, editors and reviewers as part of the solution,” Colella said.

She differentiates between the ideas of specimen “ownership” and “stewardship.”

“Specimen stewardship promotes the democratization of specimens to maximize access and research potential through the use and re-use of specimens' resources to answer multiple scientific questions, instead of private ownership for use in a single project,” Colella said. “If samples never get archived with a museum, it’s a loss to the entire scientific community. We’re saying if you have private specimen collections, there needs to be a plan to get those samples archived eventually, so that if you’re not around anymore or you need someone else to archive them, they know what to do. There needs to be a plan from the very beginning when the specimens are collected. Stewardship is making sure that the resources you’re collecting are taken care of into the future and museum exist to do just that.”

Wednesday, December 16, 2020

LAWRENCE — University Distinguished Professor Jorge Soberón has been named interim director of the Biodiversity Institute & Natural History Museum at the University of Kansas.

“Dr. Soberón is an internationally recognized leader in biodiversity modeling. He is well known for both his scholarship and his collegiality,” said Simon Atkinson, vice chancellor for research. “I have every confidence that he will lead the Biodiversity Institute well during this time of transition.”

Soberón is a professor in KU’s Department of Ecology & Evolutionary Biology and a senior scientist in biodiversity modeling at the Biodiversity Institute. He will step into a leadership role held for 25 years by Leonard “Kris” Krishtalka, who is retiring at the end of this year. The search for a permanent director is ongoing.

The Biodiversity Institute is an internationally recognized center for research and graduate education in systematics, evolutionary biology, paleontology and archaeology. The KU Natural History Museum is the iconic public face of the institute and serves public audiences including K-12 schools, families and adults, the university and the informal science education community.

Soberón joined KU in 2005 and was appointed a University Distinguished Professor in fall 2014. He is a world-renowned scholar in interdisciplinary biodiversity science and ecology, and his research focuses on documenting and understanding large-scale spatial patterns in the biodiversity of terrestrial species. Indeed, he has been pivotal in establishing KU as a world leader in the field of biodiversity informatics. His research themes include theoretical and computational modeling of species’ richness across landscapes, and the past, present and future geographic distributions of species under scenarios of environmental change as well as the international policy implications of those changes. Soberón’s research has been funded by major grants from the National Science Foundation and Microsoft Research, and his papers have been published in the highest-ranking journals in his field.

He earned a doctorate from Imperial College, University of London, in 1982 and holds bachelor’s and master’s degrees from the National University of Mexico. In 2018, Soberón was awarded a Silver Medal by the Mexican government as one of 31 “Distinguished Mexicans” who are living outside Mexico.

The University of Kansas is a major comprehensive research and teaching university. The university's mission is to lift students and society by educating leaders, building healthy communities and making discoveries that change the world. The KU News Service is the central public relations office for the Lawrence campus.

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Wednesday, August 12, 2020

KU herpetology researcher and colleagues handling a snake in the field
The successful candidate will provide visionary leadership that will guide the faculty, staff and students of this designated research center and public museum to its next phase of achievement.
Information | Position Profile | Apply

The University of Kansas seeks outstanding applicants for the position of director of its Biodiversity Institute & Natural History Museum. The director sets the strategic direction for the BI with regard to research, education and outreach and holds a 20% joint appointment as a tenured faculty member in an appropriate academic department. The director has unique opportunities to develop a personal research program synergistically within the BI and collaboratively with a large and diverse KU research community. This is an endowed directorship. Funds from the endowment provide the director with additional resources to advance the BI’s mission. The formal name of the directorship will be announced in 2021. ABOUT THE BI/NHM The KU Biodiversity Institute is an internationally recognized center for research and graduate education in systematics, evolutionary biology, paleontology and archaeology. In addition to the collection and curation of recent and fossil animals and plants, the BI is a world leader in the field of biodiversity informatics, including the development of global data architectures and platforms for the processing and research analysis of species data.

The KU Natural History Museum is the iconic public face of the BI and serves public audiences including K-12 schools, families and adults, the university, and the informal science education community. The Natural History Museum shares, interprets and educates diverse audiences about the natural world through engaging and innovative exhibits, programming and projects. The ideal candidate will contribute to the collective goals of the Biodiversity Institute & Natural History Museum:

1. To maintain and improve collections to meet the research, educational and service needs of scientists, students, the public and agencies of the public.

2. To enhance research and graduate education programs so they represent the breadth, scientific rigor and promise of systematic and evolutionary biology and archaeology.

3. To increase participation in the relevant academic programs of the university, principally within the departments of Ecology and Evolutionary Biology, Geology, and Anthropology, and the Museum Studies Program.

4. To continue developing public education and related services in ways that encourage public understanding and appreciation of the natural world.

5. To increase understanding and support of the museum through public relations, membership, development programs and the activities of the Biodiversity Institute Advisory Board. The Biodiversity Institute consists of the divisions of Archaeology, Biodiversity Modeling, Botany (McGregor Herbarium), Entomology, Herpetology, Ichthyology, Informatics, Invertebrate Paleontology, Invertebrate Zoology, Mammalogy, Ornithology, Paleobotany and Vertebrate Paleontology. These divisions collaborate with the departments of Ecology and Evolutionary Biology, Geology, and Anthropology, and the Museum Studies Program in research, education and public service programs. The Biodiversity Institute employs 20 (11.5 FTE) curators and research scientists, many of whom are on joint appointments in related academic departments, along with 19 adjunct, courtesy and emeritus faculty. They collectively provide a rich intellectual resource for the museum’s 4 postdoctoral staff, 44 graduate students and 50 undergraduate students. 

The Biodiversity Institute also employs 10 professional collection care and support staff (9.75 FTE); 6 public programs staff (6.0 FTE); and 5 administrative staff (5.0 FTE).

Founded in 1865, the University of Kansas is an R1-rated public research university with more than 40 graduate programs ranked by U.S. News & World Report. KU enrolls 28,500 students and employs nearly 2,900 faculty members across five campuses (Lawrence, Kansas City, Overland Park, Wichita and Salina).

Including the BI, the Office of Research oversees 10 university research centers, two state surveys and about a dozen core laboratories. Faculty and staff on all KU campuses generated $263.9 million in externally funded research expenditures in FY2019. Collectively, that activity fuels KU’s mission to be an institution “making discoveries that change the world.” It’s also among the reasons KU retains membership in the prestigious Association of American Universities — one of just 36 U.S. public institutions among 65 that are transforming lives through education, research and innovation.

As a premier international research university, KU is committed to an open, diverse, and inclusive learning and working environment that nurtures the growth and development of all. KU holds steadfast in the belief that a variety of values, interests, experiences, and intellectual and cultural viewpoints enrich learning and our workplace. The university actively seeks applications from members of groups underrepresented in higher education.

Administrative duties
The director provides leadership in strategic planning and organizational structure while facilitating and executing the mission of the BI. Administrative duties include preparing and evaluating the budget; managing and distributing annual operating funds, endowment income and other funds beyond state allocations; preparing annual reports, mission statements and other documents requested by the Vice Chancellor for Research; recruting and retaining top talent; and conducting performance evaluations of academic and unclassified professional staff, ensuring a community of collegiality and excellence. The director fosters the professional development of collections care; coordinates activities among divisions, presides over meetings of the advisory board; and represents the BI to the university and systematics communities, external agencies, and the public.

Research and education
The director facilitates the education and research mission of the BI and promotes an open, diverse and inclusive learning and working environment that nurtures the growth and development of students, staff, affiliates and visitors. The director fosters the intellectual growth and development of graduate and undergraduate students associated with the BI, cooperates with degree-granting departments and enhances support of students. The director may sponsor graduate students and serve on graduate student committees.

The director furthers the development of the BI as an international center for collections-based research, knowledge dissemination, and information technology by encouraging and advocating for high-quality research in systematic biology and related fields, and obtains a broad understanding of the role of the BI in the university community and natural sciences. The position is expected to assess priorities of current research and the directions of future research for the unit. The director promotes the free interchange of ideas and provides intellectual leadership to the BI community and promotes appropriate use of the BI’s resources and information by governmental and private agencies. The director is encouraged to maintain an independent program of research and scholarly productivity.

Exhibits and public programs
The director supports the museum’s education, outreach, and exhibit programs. The director furthers the contribution of the KU Natural History Museum to the education and service missions of the BI and the broader university, as well as to the field of informal science education. The director advocates on behalf of the museum at the university state and regional levels and promotes collaboration with other KU entities and external organizations.

Collections development and stewardship
The director encourages the advancement of state-ofthe-art practices in the care of the BI’s collections to ensure the collections and their associated data are valued for research, education and service. The director promotes the visibility, engagement and awareness of the value of the BI’s collections to campus state, and international stakeholders. The director advances short- and long-term strategies for collections storage, access and curation. The director promotes responsible collection growth and cultivates BI collections leadership in international cyberinfrastructures.

The director provides strong leadership and active engagement in strengthening the financial resources available, and in building a broad base of support for the BI and KU Natural History Museum within and outside the university. The director should be an effective advocate for the BI to the university administration, KU Endowment, KU Alumni and outside the university. The director should aggressively pursue external funding from federal, state and local government, community and foundation-based sources. The director should encourage maximum use of the resources of the BI Advisory Board and membership, and encourage an innovative, entrepreneurial approach in marketing the museum to the public.

Faculty responsibilities
The director serves as a tenured, full professor in the appropriate academic unit with a 20% appointment. Tenured faculty members are expected to meet satisfactory standards of performance in three areas of responsibility — teaching/advising, research and service — and to carry out those responsibilities in accordance with the Faculty Code of Rights, Responsibilities & Conduct. In a given year, contributions to teaching/advising, research and service may be balanced, or added emphasis may be placed on one or more components.

Evaluation of the following requirements will be made through (1) description of work experience and educational experiences in CV and (2) record of accomplishments and productivity addressed in CV:

1. Doctorate degree from an accredited college or university and eligibility for tenured appointment at the rank of full professor in Ecology & Evolutionary Biology or a related academic department.
2. Experience serving as an academic leader and team builder, developing and enhancing research and educational relationships among faculty, staff, alumni and affiliated units/partners.
3. Demonstrated teaching experience at both the undergraduate and graduate levels and a commitment to teaching excellence.
4. Demonstrated record of scholarly achievement in a field related to biodiversity, as demonstrated by refereed publications and/or research grants with the promise of continued activity.
5. Demonstrated experience in the administration of an organization, including the management oversight of finances, personnel and program development.
6. Evidence of obtaining financial support through competition for public or private sources.
7. Excellent communication skills as demonstrated through application materials and interviews.
8. Experience working with multidisciplinary constituencies.
9. Record of promoting diversity, equity, accessibility and inclusion.

1. At least five years administrative experience, including budgeting, personnel management and program development.
2. Demonstrated vision for the future of collections-based research and the role of museums. 
3. Demonstrated knowledge of museum operations, including collection management, public education, exhibits, and research.
4. Demonstrated professional association with the national and international museum community as evidenced by a record of service in a museum or through museum activities of an appropriate professional organization.
5. Experience in graduate or undergraduate mentoring in a scientific discipline or museum studies program.
6. Administrative experience in a comprehensive doctoral degree-granting university, university museum, or other natural history museum.
7. Administrative-level knowledge of subdisciplines of biodiversity informatics and the international biological museum data community.
8. Record of entrepreneurial leadership.

Application review begins August 31, 2020

Wednesday, October 30, 2019

Leo Smith, associate curator of ichthyology at the University of Kansas Biodiversity Institute and Natural History Museum, and associate professor in the Department of Ecology and Evolutionary Biology, recently had two photographs honored as Images of Distinction in the 45th annual 2019 Nikon Small World Photo Competition. The international contest honors the best images that showcase the “beauty and complexity of life as seen through the light microscope.”

Anoplogaster cornura (deep-sea Fangtooth) fish skeleton

In 2018, Smith led a KU team that pioneered new techniques for the imaging of vertebrate skeletons. Building on existing techniques to remove specimen tissue while leaving cartilage and skeletal structures intact for study, Smith's process significantly refined specimen images through the use of gelatin and glycerin to pose specimens and to visualize the skeleton through fluorescence microscopy. The alizarin dye that stains the calcium in bones fluoresces red under the right light wavelengths, highlighting the skeletal structure with dramatic detail. This process was used with both of Smith's winning images which depict a fluorescently- stained Anoplogaster cornuta (deep-sea Fangtooth) skeleton (top image) and the fluorescently stained skull of a Lepisosteus osseous (longnose gar) fish (at left). 

View Leo Smith's images on the Nikon website:
Anoplogaster cornuta (deep-sea Fangtooth) skeleton
Lepisosteus osseous (longnose gar) fish

View all award winners on the Nikon website. 

Tuesday, August 13, 2019

Jennifer Giron collecting aquatic beetles in Suriname

LAWRENCE — Researchers from the University of Kansas have described three genera and 17 new species of water scavenger beetles from the Guiana and Brazilian Shield regions of South America, areas seen as treasure houses of biodiversity. The beetles from the countries of French Guiana, Suriname, Brazil, Guyana and Venezuela were discovered through fieldwork and by combing through entomological collections at the Smithsonian Institution and KU.

The beetles are described in a new paper in ZooKeys, a peer-reviewed journal. 

Lead author Jennifer Girón, a KU doctoral student in ecology & evolutionary biology and the Division of Entomology at KU’s Biodiversity Institute, said the new species hint at vast biodiversity left to be described in regions where resource-extraction operations today are destroying huge swaths of natural habitat.


“The regions we've been working on, like Venezuela and Brazil, are being degraded by logging and mining,” she said. “Eventually, they’re going to be destroyed, and whatever lives there is not going to be able to survive. At this point, we don't even know what’s there — there are so many different kinds of habitats and so many different resources. The more we go there, and the more we keep finding new species, the more we realize that we know next to nothing about what’s there.”

According to Girón and co-author Andrew Short, associate professor of ecology & evolutionary biology at KU, fieldwork and taxonomic work on Acidocerinae (a subfamily of the family Hydrophilidae of aquatic beetles) during the past 20 years have exposed “an eye-opening diversity of lineages and forms resulting in the description of seven of the 11 presently recorded genera since 1999.”

The KU researchers said the three new genera they’ve now added to Acidocerinae possibly have remained obscure until now because many of the species inhabit seepages — areas where groundwater rises to the surface through mud or flow over rocks near rivers or streams.

Girón and Short discovered some of the new species during a field trip to Suriname.

“I have only been to one of the expeditions there,” Girón said. “Before that, I had no experience collecting aquatics. But Andrew (Short) has been to those places many times. It’s very remote, in the heart of the jungle. We went four hours in a bus and then four more hours in a boat up the river. There is a field station for researchers to go and stay for a few days there. We looked for the beetles along the river, forest streams and also in seepages.”  

During their fieldwork, Girón and Short, along with a group of KU students, sought the seepages that were rich hunting grounds for acidocerine aquatic beetles.

“If you’re along a big river, you're not as likely to find them,” Girón said. “You have to find places where there’s a thin layer of running water or small pools on rocks. They’re more common around places with exposed rock, like a rock outcrop or a cascade. These habitats have been traditionally overlooked because when you think of collecting aquatic beetles or aquatic insects in general, you think of rivers or streams or ponds or things like that — you usually don't think about seepages as places where you would find beetles. So usually you don't go there. It’s not that these aquatic beetles are especially rare or hard to find. It's more like people usually don’t collect in these habitats.”

Girón said the descriptions of the new aquatic beetles also underscore the usefulness of museum collections to ongoing scientific research in biodiversity.

“It's important to highlight the value of collections,” she said. “Without specimens housed in collections, it would be impossible to do this kind of work. Nowadays, there has been some controversy about whether it is necessary to collect specimens and deposit them in collections in order to describe new species. Every person that has ever worked with collections will say, ‘Yes, we definitely need to maintain specimens accessible in collections.’ But there are recent publications where authors essentially just add a picture of one individual to their description without actual specimens deposited in collections, and that can be enough for them to publish a description. The problem with that is there would be no reference specimens for detailed comparisons in the future. For people who do taxonomic work and need to compare many specimens to define the limits of different species, one photo is not going to be enough.”

To differentiate and classify the new species, Girón and Short focused on molecular data as well as a close examination of morphology, or the bodies of the aquatic beetles.

“This particular paper is part of a bigger research effort that aims to explain how these beetles have shifted habitats across the history of the group,” Girón said. “It seems like habitat has caused some morphological differences. Many aquatic beetles that live in the same habitats appear very similar to each other — but they’re not necessarily closely related. We’ve been using molecular techniques to figure out relationships among species and genera in the group.”

Girón, who grew up in Colombia and earned her master’s degree in Puerto Rico, said she hoped to graduate with her KU doctorate in the coming academic year. After that, she will continue her appointments as research associate and acting collections manager at the Natural Science Research Laboratory of the Museum of Texas Tech University.

-- by Brendan Lynch, KU News
Original KU News link

Top image: Jennifer Girón, a KU doctoral student in ecology & evolutionary biology and the Division of Entomology at KU’s Biodiversity Institute, collecting aquatic beetles during fieldwork in Suriname. Credit: Andrew Short 


Thursday, June 20, 2019

traitomine dataLAWRENCE — New research from the University of Kansas shows machine learning is capable of identifying insects that spread the incurable disease called Chagas with high precision, based on ordinary digital photos. The idea is to give public health officials where Chagas is prevalent a new tool to stem the spread of the disease and eventually to offer identification services directly to the general public. 

Chagas is particularly nasty because most people who have it don’t know they’ve been infected. But according to the Centers for Disease Control and Prevention, some 20 percent to 30 percent of the 8 million people with Chagas worldwide are struck at some later point with heart rhythm abnormalities that can bring on sudden death; dilated hearts that don’t pump blood efficiently; or a dilated esophagus or colon.

The disease is caused most often when triatomine bugs — more commonly known as “kissing bugs” — bite people and transmit the parasite Trypanosoma cruzi into their bloodstreams. Chagas is most prevalent in rural areas of Mexico, Central America and South America.

A recent undertaking at KU, called the Virtual Vector Project, sought to enable public health officials to identify triatomine that carry Chagas with their smartphones, using a kind of portable photo studio for taking pictures of the bugs. 

Now, a graduate student at KU has built on that project with proof-of-concept research showing artificial intelligence can recognize 12 Mexican and 39 Brazilian species of kissing bugs with high accuracy by analyzing ordinary photos — an advantage for officials looking to cut the spread of Chagas disease.

Ali Khalighifar, a KU doctoral student at the Biodiversity Institute and the Department of Ecology and Evolutionary Biology, headed a team that just published findings in the Journal of Medical Entomology. To identify the kissing bugs from regular photos, Khalighfar and his colleagues worked with open-source, deep-learning software from Google, called TensorFlow that is similar to the technology underpinning Google’s reverse image search.

“Because this model is able to understand, based on pixel tones and colors, what is involved in one image, it can take out the information and analyze it in a way the model can understand — and then you give them other images to test and it can identify them with a really good identification rate,” Khalighifar said. “That’s without preprocessing — you just start with raw images, which is awesome. That was the goal. Previously, it was impossible to do the same thing as accurately and certainly not without preprocessing the images.”

Khalighifar and his coauthors — Ed Komp, researcher at KU’s Information and Telecommunication Technology Center, Janine M. Ramsey of Mexico’s Instituto Nacional de Salud Publica, Rodrigo Gurgel-Gonçalves of Brazil’s Universidade de Brasília, and A. Townsend Peterson, KU Distinguished Professor of Ecology and Evolutionary Biology and senior curator with the KU Biodiversity Institute — trained their algorithm with 405 images of Mexican triatomine species and 1,584 images of Brazilian triatomine species.

At first, the team was able to achieve, “83.0 and 86.7 percent correct identification rates across all Mexican and Brazilian species, respectively, an improvement over comparable rates from statistical classifiers,” they write. But after adding information about kissing bugs’ geographic distributions into the algorithm, the researchers boosted the accuracy of identification to 95.8 percent for Mexican species and 98.9 percent for Brazilian species. 

According to Khalighifar, the algorithm-based technology could allow public health officials and others to identify triatomine species with an unprecedented level of accuracy, to better understand disease vectors on the ground.

“In the future, we’re hoping to develop an application or a web platform of this model that is constantly trained based on the new images, so it’s always being updated, that provides high-quality identifications to any interested user in real time,” he said.

Khalighifar now is applying a similar approach using TensorFlow for instant identification of mosquitoes based on the sounds of their wings and frogs based on their calls.

“I’m working right now on mosquito recordings,” he said. “I’ve shifted from image processing to signal processing of recordings of the wing beats of mosquitoes. We get the recordings of mosquitoes using an ordinary cell phone, and then we convert them from recordings to images of signals. Then we use TensorFlow to identify the mosquito species. The other project that I’m working right now is frogs, with Dr. Rafe Brown at the Biodiversity Institute. And we are designing the same system to identify those species based on the calls given by each species.” 

While often artificial intelligence is popularly portrayed as a job-killing threat or even an existential threat to humanity, Khalighifar said his research showed how AI could be a boon to scientists studying biodiversity.

“It’s amazing — AI really is capable of doing everything, for better or for worse,” he said. “There are uses appearing that are scary, like identifying Muslim faces on the street. Imagine, if we can identify frogs or mosquitoes, how easy it might be to identify human voices. So, there are certainly dark sides of AI. But this study shows a positive AI application — we’re trying to use the good side of that technology to promote biodiversity conservation and support public health work.”

-- by Brendan Lynch, KU News Service
Original article link


Wednesday, June 26, 2019

white-breasted guinea fowl - photo by Benedictus FreemanLAWRENCE — Growing up in Liberia during that country’s brutal 14-year civil war, Benedictus Freeman and his family fled into the rainforest, where they survived for years eating bush meat and foraging. The rainforest provided Freeman sustenance and protection — but more than that, the experience ignited a passion in him for understanding and preserving nature.

“At that time, I really didn’t know how important the forest would become for me — I saw the forest as a source of resources like food and shelter,” said Freeman, who today is a doctoral student in ecology & evolutionary biology at the University of Kansas and KU Biodiversity Institute. “But I developed an interest in nature there, and eventually I started studying forestry for my undergraduate degree. That actually influenced my decision to get more interested in nature and conservation.”

The rainforests that once protected Freeman and his family host one of West Africa’s flagship bird species — the White‐breasted Guineafowl (Agelastes meleagrides). Now, Freeman is lead author of a new paper in the peer-reviewed journal Avian Research that projects the geographic distribution of the bird through 2050 as it shifts habitat due to climate change.

“This bird is endemic to West Africa, but it’s not fully understood — it’s poorly studied,” Freeman said. “Because of this poor history, there’s very little understanding about its range. Our study recharacterizes its distribution and helps us to understand to what extent it’s distributed across the region. The bird is threatened, and it’s of conservation concern. So that’s why it was selected for study.”

According to Freeman, the vulnerable White-breasted Guineafowl, which has appeared on Liberian postage stamps, serves as an iconic “flagship species,” conservation of which could preserve habitat of many lesser-known animals at the same time.

The KU researcher said West Africa suffers from extensive deforestation due to increasing populations, urbanization, agriculture expansion (both substance farming and industrial-scale farming of palm oil), logging and mining. Because of its exclusive dependence on the forest for habitat, the White-breasted Guineafowl is particularly susceptible to habitat loss.

“It occurs within rainforest habitats in West Africa where it feeds like regular birds, like chickens feed, and depends on insects and seeds and things,” Freeman said. “The important thing about this bird is that it’s a specialist — it’s more restricted to rainforest habitats. There is a sister species (Black Guineafowl, Agelastes niger) of the same bird that occurs on the other side of the Guinean forest, but this one is range-restricted, and it’s only found in this region. It’s not going to be found anywhere else in the world.”

Freeman hopes his research predicting the distribution of the bird in coming decades can help inform policymakers about which areas of rainforest should be prioritized for conservation.

For the new paper, Freeman and his colleagues — Daniel Jiménez‐García of Benemérita Universidad Autónoma de Puebla in Mexico, Benjamin Barca of the Royal Society for the Protection of Birds in Sierra Leone and Matthew Grainger of  Newcastle University in the United Kingdom — used occurrence data from the Global Biodiversity Information Facility and datasets about occurrences of the White-breasted Guineafowl in Sapo National Park in Liberia and Gola Rainforest National Park in Sierra Leone, including data collected by Freeman.

The authors used environmental datasets from NASA and other open sources to perform ecological niche modeling, which the researchers said “integrates known occurrences of species and environmental variables (e.g., temperature, precipitation) to characterize potential future geographic distributions of species in response to global climate change.”

The team created maps showing current and likely future habitats where the White‐breasted Guineafowl could migrate in response to a shifting climate. Unexpectedly, there was good news for the iconic bird in the findings: “The projected impacts of climate change on the geographic distribution of White-breasted Guineafowl were minimal, suggesting stability across the species’ range for the present and in the future, at least as regards climate change effects,” researchers said. “Low sensitivity to climate change in this species does match the general observation for West African birds.”

However, the team found coastal areas where the White‐breasted Guineafowl is found today would be degraded by sea-level rise and resulting coastal erosion, destroying some of the species’ range.

As for Freeman, this summer he’s back in Liberia conducting more fieldwork on birds in some of the same areas his team found to be suitable for the White-breasted Guineafowl.

"We were pleased to document populations at the sites where we worked, and then we were able to collect data on other bird species,” he said. “We have some interesting records that might be species not yet known to science, but we need to do some detailed studies."

Freeman aims to finish his doctorate at KU next year, he said. After that, he’ll look for opportunities for postdoctoral work.

“I don’t know exactly where that’s going to be,” he said. “But I’m hoping that wherever I get a good job, I can have an opportunity to work in West Africa to do more research. There’s a huge capacity gap in that area. There’s a need to have homegrown scientists involved with this kind of research specifically. So, my passion is to work there.”

-- by Brendan Lynch, KU News
Original KU News link

Top photo: White-breasted Guineafowl. Credit: Benedictus Freeman

Monday, April 1, 2019

tangled mass of articulated fish from the Tanis inundation surge depositA study to be published Monday in the Proceedings of the National Academy of Sciences offers a scientific first: a detailed snapshot of the terrible moments right after the Chicxulub impact — the most cataclysmic event known to have befallen life on Earth.

At a site called Tanis in North Dakota’s Hell Creek Formation, a team of paleontologists whose headquarters are at the University of Kansas unearthed a motherlode of exquisitely-preserved animal and fish fossils — creatures that lived in and around a deeply chiseled river connected to the ancient Western Interior Seaway — that were killed suddenly in events triggered by the Chicxulub impact.

The fossils were crammed into a “rapidly emplaced high-energy onshore surge deposit” along the KT boundary that contained associated ejecta and iridium impactite associated with the impact about 66 million years ago — an impact that eradicated about 75 percent of Earth’s animal and plant species.

field research with Robert DePalma at left and Peter Larson at right examining the site“A tangled mass of freshwater fish, terrestrial vertebrates, trees, branches, logs, marine ammonites and other marine creatures was all packed into this layer by the inland-directed surge,” said lead author Robert DePalma, a KU doctoral student in geology who works in the KU Biodiversity Institute and Natural History Museum. “Timing of the incoming ejecta spherules matched the calculated arrival times of seismic waves from the impact, suggesting that the impact could very well have triggered the surge.”

DePalma, who discovered the fossil motherlode, said the find outlines how the impact could have devastated areas very far from the crater quite rapidly.

“A tsunami would have taken at least 17 or more hours to reach the site from the crater, but seismic waves — and a subsequent surge — would have reached it in tens of minutes,” he said.

DePalma and his colleagues describe the rushing wave that shattered the Tanis site as a “seiche.”

“As the 2011 Tohoku earthquake in Japan showed us, seismic shaking can cause surges far from the epicenter,” he said. “In the Tohoku example, surges were triggered nearly 5,000 miles away in Norway just 30 minutes after impact. So, the KT impact could have caused similar surges in the right-sized bodies of water worldwide, giving the first rapid ‘bloody nose’ to those areas before any other form of aftermath could have reached them.”

According to KU researchers, even before the surge arrived, Acipenseriform fish (sturgeon) found at the site already had inhaled tiny spherules ejected from the Chicxulub impact.

micro-CT image showing cutaway of clay-altered ejecta spherule with internal core of unaltered impact glass“The fish were buried quickly, but not so quickly they didn’t have time to breathe the ejecta that was raining down to the river,” said co-author David Burnham, preparator of vertebrate paleontology at the KU Biodiversity Institute. “These fish weren’t bottom feeders, they breathed these in while swimming in the water column. We’re finding little pieces of ejecta in the gill rakers of these fish, the bony supports for the gills. We don’t know if some were killed by breathing this ejecta, too.”

The number and quality of preservation of the fossils at Tanis are such that Burnham dubs it the “lagerstätte” of the KT event — paleontologist-speak for a landmark sedimentary deposit with exceptionally intact specimens. He said this is especially true as the fish are cartilaginous, not bony, and are less prone to fossilization.

“The sedimentation happened so quickly everything is preserved in three dimensions — they’re not crushed,” Burnham said. “It’s like an avalanche that collapses almost like a liquid, then sets like concrete. They were killed pretty suddenly because of the violence of that water. We have one fish that hit a tree and was broken in half.”

Indeed, the Tanis site contains many hundreds of articulated ancient fossil fish killed by the Chicxulub impact’s aftereffects and is remarkable for the biodiversity it reveals alone.

“At least several appear to be new species, and the others are the best examples known of their kind,” DePalma said. “Before now, fewer than four were known from the Hell Creek, so the site was already magnificently significant. But we quickly recognized that the surrounding sediment was deposited by a sudden, massive rush of water, and that the surge was directed inland, away from an ancient nearby seaway. When we noticed asteroid impact debris within the sediment and a compact layer of KT boundary clay resting on top of it from the long-term fallout, we realized that this unusual site was right at the KT boundary.”

According to Burnham, the fossil trove fills a void in scientific knowledge with vivid new detail.

Researchers at the site posing: Jan Smit, Robert DePalma, Walter Alvarez and David Burnham wit a box core sample“We’ve understood that bad things happened right after the impact, but nobody’s found this kind of smoking-gun evidence,” he said. “People have said, ‘We get that this blast killed the dinosaurs, but why don’t we have dead bodies everywhere?’ Well, now we have bodies. They’re not dinosaurs, but I think those will eventually be found, too.”

DePalma said his find provides spectacular new detail to what is perhaps the most important event to ever affect life on Earth.

“It’s difficult not to get choked up and passionate about this topic,” he said. “We look at moment-by-moment records of one of the most notable impact events in Earth’s history. No other site has a record quite like that. And this particular event is tied directly to all of us — to every mammal on Earth, in fact. Because this is essentially where we inherited the planet. Nothing was the same after that impact. It became a planet of mammals rather than a planet of dinosaurs.

"As human beings, we descended from a lineage that literally survived in the ashes of what was once the glorious kingdom of the dinosaurs. And we’re the only species on the planet that has ever been capable of learning from such an event to the benefit of ourselves and every other organism in our world.”

At KU, DePalma and Burnham worked with Loren Gurche of the Biodiversity Institute. Other co-authors are Jan Smit and Klaudia Kuiper of VU University Amsterdam; Phillip Manning of the University of Manchester; Anton Oleinik of Florida Atlantic University; Peter Larson of the Black Hills Institute of Geological Research Inc.; Florentin Maurrasse of Florida International University; Johan Vellekoop of VU Leuven; and Mark A. Richards and Walter Alvarez of the University of California at Berkeley. 

-- by Brendan Lynch, KU News
Original KU News link 

Images: Top, intertangled mass of articulated fish from the Tanis inundation surge deposit. Middle top, Robert DePalma and Peter Larson conduct field research in Tanis. Middle bottom, micro-CT image showing cutaway of clay-altered ejecta spherule with internal core of unaltered impact glass. Bottom, researchers from left to right, Jan Smit, Robert DePalma, Walter Alvarez, David Burnham, with a collected box core sample of the KT boundary from Tanis. Images courtesy Robert DePalma.

Vertebrate Paleontology
Thursday, January 25, 2018

lizard Luperosaurus cumingii

A new paper appearing in Proceedings of the Royal Society B shows a varied collection of lizards throughout Asia to be unexpectedly close cousins of beach-dwelling mourning geckos, all descended from a common ancestor species that thrived along an ancient archipelago in the West Pacific that served as a “superhighway” of biodiversity.

The dispersal of these lizards, of the genus Lepidodactylus, touches upon a major theory of island biogeography developed by celebrated biologist E.O. Wilson, dubbed the “taxon cycle” model. The new paper also sheds light on lineage diversity and habitat use in the world’s most geologically complex insular region — Pacific island arcs spanning from the Philippines to Fiji.

“One of the things that I find exciting about this work is how our phylogeny, estimated from DNA sequence data, provides evidence for a giant, widespread radiation of variably sized mourning geckos, scaly-toed geckos and their relatives,” said co-author Rafe Brown, professor of ecology & evolutionary biology and senior curator at the KU Biodiversity Institute. “It was a big surprise to find groups of large-bodied, morphologically diverse, deep forest specialists, nested within a widespread clade of small-bodied coastal generalists — we didn’t think they were related at all.”

Brown said some of the mourning geckos’ closest relatives are physically very different, but all “conspicuously” live along island arcs or lost island arcs that have merged into continents, including the modern-day Philippines, northern and eastern New Guinea, eastern Melanesia, Vanuatu, Fiji, Christmas Island and Borneo.

Of 12 major Lepidodactylus lineages, interesting groups include a genus of obligate forest “slender gecko” species and two groups of mysterious “flap-legged” geckos endemic to the Philippines.

“The slender, long-bodied geckos of the genus Pseudogekko live deep in forests, and we didn’t think they were related to the small, primarily coastal scaly-toed geckos,” Brown said. “Another is Luperosaurus, the flap-legged geckos. They’re big and robust and have thorns and flaps all over their bodies, and some are orders of magnitude larger than mourning geckos. It’s astounding that these lizards that are so physically different have turned out to be close relatives.”

Brown’s collaborators included lead author Paul Oliver of Australian National University as well as Fred Kraus of the University of Michigan, Eric Rittmeyer of Rutgers University, Scott Travers of KU and Cameron Siler of the University of Oklahoma.

“To me, this work underscores how much we have yet to understand about the complexity of species diversification on our planet, particularly in island systems,” said Siler. “It is amazing to think about the role these ancient island systems played in the evolution of endemic communities in Wallacea, the West Pacific and Australasia.”

According to Brown, the findings were the result of extensive fieldwork among researchers as well as genetic analysis and data gleaned from biodiversity collections.

“No one research group could ever have put this together alone,” he said. “Firstly, we never knew these groups were closest relatives, and with separate research groups focusing on different regions with what we thought were unrelated lizard faunas, we might not have even put their DNA sequences into analyses together. The sheer magnitude of the sampling around New Guinea, Australasia, Borneo, Melanesia, Christmas Island, the Philippines and across the Pacific made this study possible. The key was putting together the efforts of many friends and colleagues who provided access to their samples and allowed us to paint the whole picture. Some of these lizards are super rare — there’s no way, in a single person’s career, could an individual go to all these places and collect all the necessary samples.”

Brown said the evolution of Lepidodactylus may be tied to the Vitiaz Arc, a near continuous chain of island arcs that stretched across the West Pacific some 30-40 million years ago during the Oligocene, which today is incorporated into present-day landforms ranging from the Philippines to Fiji.

“We used DNA sequencing data and sophisticated statistical analysis to estimate divergence of major groups in the phylogeny,” he said. “Those initial divergences probably date back to between 30 and 40 million years. When you scroll back into Earth’s history, the landmasses looked very different. One thing that jumps out is the inferred existence of a long chain of islands that stretched out across the Pacific called the Vitiaz Arc. This configuration of fragments of modern-day landmasses and islands that have since shifted but once lined up like a kind of superhighway for biodiversity across the Pacific. Given the timing, it seems like that big long chain of islands may have played a role in the evolution of this group.”

Brown said as the Vitiaz Arc fragmented and parts turned into the Philippines, Solomons, Fiji, Vanuatu and other islands that today are all very far apart, they may have facilitated the broad distribution of Lepidodactylus. 

“If ancient lineages evolved and gained widespread distribution across this ancient arc, some really may have persisted for the past 30 to 40 million years,” he said. 

The dispersal of the Lepidodactylus touches upon the model of the “taxon cycle” proposed by E.O. Wilson in his study of ants in Fiji and New Guinea. Wilson’s idea was that colonizer species are specialized to survive harsh island coastal terrains but eventually evolve traits to adapt to habitats away from island margins — more inland and upland — where some successor species thrive and others go extinct. In the meantime, the original costal colonizers often are replaced by successive waves of new invaders. 

“It’s a very famous, influential idea about how species may colonize new islands and habitats and possibly evolve through predictable ecological transitions,” Brown said. “The idea is very provocative because we commonly think about evolution as determined in part by chance, but what some components of species geographical range evolution were almost deterministic? The brilliance of E.O. Wilson was his ability to conceive of a cyclic process based solely on patterns he saw in ant species’ distributions. He didn’t have the phylogenies we have today, but he inferred relations and put this together as a very clear model, with predictions that we can test today with DNA, sophisticated statistics and knowledge of species’ distributions.”

According to Brown, findings in the new paper include support for the taxon cycle model in Lepidodactylus but also some evidence that runs counter to it. 

“In some cases, lizard lineages limited to continental fragments have persisted,” he said. “And in some cases, we did not find the most ancient lizards to be specialists from interior habitats on the oldest land masses. Some ancient lineages are found today on the margins of arc islands or just on the edges of larger landmasses. There are exceptions to any rule, of course. For instance, Lepidodactylus ranauensisis — a species that looks like the kind of common lizard that you might expect to find on a coconut tree on a beach in the Philippines—is actually endemic to Mount Kinabalu on Borneo, maybe 32 million years old, and has no close relatives. Perhaps it is the only surviving member of a once more diverse group of lineages that have gone extinct.  We just don’t know. But to find these single evolutionary relics is sort of exciting for a phylogeneticist.”

-- by Brendan Lynch, KU News

Photo: Luperosaurus cumingii is one species of unexpectedly related lizards inhabiting Asia. Credit: R.M. Brown