Wednesday, October 30, 2019

Photo by Leo Smith: Anoplogaster cornuta (deep-sea Fangtooth) fish skeletonLeo 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.” 

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 Dr. 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. 

Ichthyology
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.

new species of water scavenger beetles“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.”  

Giron collecting beetles in SurinameDuring 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

PHOTOS:
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 

Top right image: Some of the aquatic beetles described for the first time: Aulonochares spp.: A–C Aulonochares tubulus: A dorsal view B lateral view C ventral view. D–F Aulonochares novoairensis: D dorsal view E lateral view F ventral view. G–I Aulonochares lingulatus: G dorsal view H lateral view I ventral view. Scale bars: 5 mm. Credit: Girón, et al. 

Lower middle image: Girón collecting in Suriname. Credit: Andrew Short

Bottom right image: Distribution of Aulonochares species. Credit: Girón, et al.

Entomology
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.

triatoma dimidiata original image and one with background removed 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

IMAGES: Left, an example image of an individual of Triatoma dimidiata. (A) Raw image and (B) final image with background removed digitally. Courtesy Khalighifar, et al. Right, this image shows that with more data (such as digital images of triatomine), the accuracy of deep learning used by the KU researchers increases whereas prior techniques plateau after a certain point. Courtesy MDPI under a Creative Commons license.

Entomology
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.

Benedictus Freeman“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

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

Top right photo: University of Kansas doctoral student Benedictus Freeman. Credit: Benedictus Freeman

Bottom right image: Climatic range gains and losses for White‐breasted Guineafowl projected based on climate model projections for 2050. The top map shows potential range gains while the bottom map shows potential range losses. Credit: Benedictus Freeman, et al.

Ornithology
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

Herpetology
Thursday, October 5, 2017

LAWRENCE — There are precious few species today in the biodiversity hotspot of Madagascar that scientists can trace directly back to when all of Earth’s continents were joined together as part of the primeval supercontinent Pangea.

But a new study in the journal Scientific Reports suggests the Malagasy striped whirligig beetle Heterogyrus milloti is an ultra-rare survivor among contemporary species on Madagascar, boasting a genetic pedigree stretching back at least 206 million years to the late Triassic period. 

“This is unheard of for anything in Madagascar,” said lead author Grey Gustafson, a postdoctoral research fellow in ecology & evolutionary biology and affiliate of the Biodiversity Institute at the University of Kansas. “It’s the oldest lineage of any animal or plant known from Madagascar.”

Gustafson and his co-authors’ research compared the living striped whirligig found in Madagascar with extinct whirligig beetles from the fossil record. They then used a method called “tip dating” to reconstruct and date the family tree of whirligig beetles.

“You examine and code the morphology of extinct species the same as you would living species, and where that fossil occurs in time is where that tip of the tree ends,” he said. “That’s how you time their evolutionary relationships. We really wanted the fossils’ placement in the tree to be backed by analysis, so we could say these are the relatives of the striped whirligig as supported by analysis, not just that they looked similar.”

Gustafson noted one major hurdle for the team was the “painful” incompleteness of the fossil record for establishing all the places where relatives of the striped whirligig beetle once lived. 

“All of the fossils come from what is today Europe and Asia — we don’t have any deposits from Madagascar or Africa for this group of insects,” he said. “But they likely were very widespread.”

Today, whirligig beetles are a family of carnivorous aquatic beetles with about 1,000 known species dominated by members of a subfamily called the Gyrininae. But the Gyrininae are young upstarts compared with the striped whirligig beetle, the last remaining species of a group dominant during the time of the dinosaurs. This group according to Gustafson was decimated by the same asteroid impact that cut down the dinosaurs and caused the Cretaceous–Paleogene extinction event.

“The remoteness of Madagascar is what may have saved this beetle,” Gustafson said. “It’s the only place that still has the striped whirligig beetle because it was already isolated at the time of the Cretaceous–Paleogene extinction event — so the lineage was able to persist, and now it’s surviving in a marginal environment.”

Even today, the ageless striped whirligig beetle keeps its own company, preferring to skitter atop the surface of out-of-the-way forest streams in southeastern Madagascar — not mixing with latecomers of the subfamily Gyrininae who have become the dominant whirligig beetles on Madagascar and abroad. 

Indeed, Gustafson is one of the few researchers to locate them during a 2014 fieldwork excursion in Madagascar’s Ranomafana National Park.

“This one is pretty hard to find,” he said. “They like these really strange habitats that other whirligigs aren’t found in. We have video of them in a gulch in a mountain range clogged with branches and debris — there are striped whirligigs all over it.”

Unfortunately, the KU researcher said the remote habitats of the striped whirligig beetle in Malagasy national parks were threatened today by human activity on Madagascar.

“It’s a socioeconomic issue,” Gustafson said. “In the national park where first specimens of the striped whirligig beetle were discovered, there are local people who use the forest as a refuge for zebu cattle because they’re concerned about zebu being robbed. Their defecation can disturb the nutrient lode in aquatic ecosystems. Part of the problem is finding a way for local people to be able to make their livelihood while preserving natural ecosystems. But it’s a hard balance to strike. A lot of original forest cover also has been slashed and burned for rice-field patties to feed people.”

Gustafson hopes the primal origins of the striped whirligig beetle can draw attention to the need for protecting aquatic habitats while conceding that conservation efforts usually are aimed at bigger and more cuddly species, like Madagascar’s famous lemurs, tenrecs and other unique carnivorans.

“One of the things that invertebrate species suffer from is a lack of specific conservation efforts,” he said. “It’s usually trickle-down conservation where you find a charismatic vertebrate species to get protected areas started. But certain invertebrates will have different requirements, and right now invertebrate-specific conservation efforts are lacking. We propose the striped whirligig beetle would make for an excellent flagship species for conservation.”

- by Brendan M. Lynch, KU News

Photos, from the top: Gray Gustafson working in Madagascar; the striped whirligig beetle body and head; an illustration of a reconstruction of one of the Mesozoic whirligig beetles related to the striped whirligig examined in the study. All images courtesy Gray Gustafson.

Entomology
Thursday, October 5, 2017

I consider myself an avian taphonomist – a unique niche within the field of paleontology – as well as a science outreach specialist. I will first explain my research interests and then discuss my path to a career in science outreach.

In case the word is new to you, “taphonomy” is the study of what occurs between the death of an organism and its discovery as a fossil. I am interested in better understanding the circumstances that lead to differential preservation of avian skeletal elements, including depositional environment, scavenger activity, age- and gender-related effects, among other factors. Through my work, I try to explore what drives preservation biases in the fossil record of birds.

My research has mainly centered upon actualistic taphonomy experiments, which means that I conduct experiments with modern organisms and environs in order to make inferences about the past. For projects conducted via the University of Georgia (as a student) and via the University of Tennessee at Martin (as a faculty member), I collected humanely-killed chickens and ducks of known age, sex, and diet and put their carcasses out in different types of environments in different climate regimes. One thing that I was especially motivated to investigate was any role that medullary tissue might play in the preservation potential of avian leg bones. After the publication of Schweitzer and others in 2005 documenting possible soft-tissue preservation in a T. rex femur, I became fascinated by the concept of medullary tissue preservation. Medullary tissue is a reproductive-specific tissue in female birds that forms along the innermost layer of limb bones during the egg-laying cycle; it acts as calcium storage for production of the egg shell. Because it is formed rapidly and then utilized (broken down) rapidly, there is a net loss of calcium from females’ skeletal elements. Because of this, it might be expected that a gender-based preservation bias exists in the avian fossil record. In addition to this particular factor, my experiments have examined the roles of age (juvenile vs. adult), environment (habitat, temperature, humidity, pH, lithology, etc.), bacteria and fungi, and scavengers (including insects, invertebrates like crabs, and vertebrates like alligators, raccoons, and bobcats). Publications reporting my results are forthcoming! 

In 2016, a large review paper that my coauthors and I had been working on for about seven years was published. It morphed from a literature review for my thesis into a multivariable analysis of the roles of paleoclimate, environment, and bird body size in avian fossil preservation. It is my hope that the paper will inspire future avian taphonomy studies to improve collection of climate-related data. Understanding how climate change has impacted the avian fossil record could shed further light on questions about speciation and extinction of birds throughout time.

My other passion (and now my career) is science outreach and education. Throughout my undergraduate and graduate studies, I was involved in public outreach events with my universities, local nature centers and parks, and regional museums. After getting established in my first job – which was as a geology instructor at the University of Tennessee at Martin – I became motivated to engage underserved K-12 girls in the community and so I began leading a science-focused Girl Scout troop. My move in 2015 to the Florida Museum of Natural History brought me even further into the world of public outreach and education as the coordinator of a project funded by the National Science Foundation called FOSSIL: Fostering Opportunities for Synergistic STEM with Informal Learners. In this role, I’ve been able to help develop and lead paleontology workshops, foster connections between amateur and professional paleontologists across the world, and collaborate on science education research. (Learn more about FOSSIL by clicking here). Organizing opportunities for people to share with others their paleontology skills, experiences, and enthusiasm has been enormously rewarding. In mid-August of this year, I’ll be starting a new job with the University of Kansas Biodiversity Institute & Natural History Museum as their Outreach and Engagement Coordinator. I’m really excited about continuing to work with the public in a new capacity to foster a greater understanding of science and an appreciation for the Earth and its history.

Being creative, asking questions, and devising ways to get others excited about science (most often about paleontology) are all aspects of my jobs that I have loved. If you’re interested in pursuing a career in science, know that there are a wide variety of different positions and career paths, so keep your options open! Explore your curiosities and read, read, read as many peer-reviewed papers as possible.

- written for Time Scavengers 

Top Left: Examining Late Plestocene avian fossils in a cave on Royal Island, Bahamas

Bottom Right: Interacting with young visitors at the Aurora Fossil Festival in Aurora, North Carolina, as part of the FOSSIL Project

Museum Staff
Tuesday, October 3, 2017

LAWRENCE — Evolutionary biologists long have supposed that when species colonize new geographic regions they often develop new traits and adaptations to deal with their fresh surroundings. They branch from their ancestors and multiply in numbers of species.

Apparently, this isn’t the story of “true frogs.” The frog family scientists call Ranidae are found nearly everywhere in the world, and their family includes familiar amphibians like the American Bullfrog and the European common frog. 

New research from the University of Kansas appearing in Royal Society Biology Letters shows, in contrast to expectations, “the rapid global range expansion of true frogs was not associated with increased net-diversification.”

“First, we had to identify where these true frogs came from and when they started their dispersal all over the world,” said lead author Chan Kin Onn, a doctoral student at KU’s Biodiversity Institute. “We found a distinct pattern. The origin of these frogs was Indochina — on the map today, it’s most of mainland Asia, including Thailand, Vietnam, Cambodia and Burma. True frogs dispersed throughout every continent except Antarctica from there. That’s not a new idea. But we found that a lot of this dispersal happened during a short period of time — it was during the late Eocene, about 40 million years ago. That hadn’t really been identified, until now.”

Next, Chan and co-author Rafe Brown, curator-in-charge of the KU Biodiversity Institute’s Herpetology Division, looked to see if this rapid dispersal of true frogs worldwide triggered a matching eruption of speciation. 

“That was our expectation,” Chan said. “We thought they’d take off into all this new habitat and resources, with no competition — and boom, you’d have a lot of new species. But we found the exact opposite was true. In most of the groups, nothing happened. There was no increase in speciation. In one of the groups, diversification significantly slowed down. That was the reverse of what was expected.”

To establish the actual timing of true frogs’ diversification, Chan and Brown performed phylogenetic analysis of 402 genetic samples obtained from an online database called GenBank. These samples represented 292 of the known 380 true frog species in the world.

“We mined all of these sequences and combined them into a giant analysis of the whole family,” Chain said. “It is to my knowledge the most comprehensive Ranidae phylogenetic analysis ever performed that included most of the representative species from the family.” 

Chan and Brown focused on four genes that would help to establish the family tree of true frogs.

“It’s a genealogical pedigree of specimens, a family tree of species,” Chan said.  “Normally, you think of family tree as everyone in one family and how the various people are related. But this is more expanded where we look at how species are related to each other, so you can trace ancestry back in time.”

After completing the phylogenetic analysis, the KU researchers used several frog fossils to “time calibrate” the history of the frogs’ global dispersal.

“We use fossil frogs because we can accurately date the fossils,” Chan said. “We know we found the fossil in a certain rock deposit, and we know with confidence how old the deposit is, so then we can estimate the age of the fossil.”

After Chan and Brown deduced similarities between fossilized true frogs as reported by paleontologists and contemporary true frogs, they placed fossils into groups of closely related species, which scientists call genera.

“Using data from paleontological studies, we can loosely place a fossil where in the phylogeny it belongs and can put a time stamp on that point,” Chan said. “That’s where calibration happens, each fossil is sort of like an anchor point. You can imagine with a really big phylogeny, the more anchor points or calibration points the better your time estimate.”

Through this process, the KU researchers concluded true frogs didn’t become one of the most biodiverse frog families due to dispersing into new ranges, or due to filling a gap created by a catastrophic die-off (such as the Eocene-Oligocene Extinction Event that triggered widespread extinctions from marine invertebrates to mammals in Asia and Europe).

Rather, the rich diversity of species in the Ranidae family comes from millions of years’ worth of continual evolution influenced by a host of different environs.  

“Our conclusion is kind of anticlimactic, but it’s cool because it goes against expectations,” Chan said. “We show the reason for species richness was just a really steady accumulation of species through time — there wasn’t a big event that caused this family to diversify like crazy.”

- Brendan M. Lynch, KU News

Top image: KU researchers concluded true frogs didn’t become one of the most biodiverse frog family due to dispersing into new ranges, or due to filling a gap created by a catastrophic die-off. Rather, the rich diversity of species in the Ranidae family comes from millions of years’ worth of continual evolution influenced by a host of different environs. Image by R.M. Brown.
From top right: The Rana igorota; Sangirana tipanan; Spotted stream (an Asian true frog); another Asian true frog. Photos courtesy of Chan Kin Onn, a doctoral student at KU’s Biodiversity Institute.

Herpetology
Tuesday, October 3, 2017

LAWRENCE — Evolutionary biologists long have supposed that when species colonize new geographic regions they often develop new traits and adaptations to deal with their fresh surroundings. They branch from their ancestors and multiply in numbers of species.

Apparently, this isn’t the story of “true frogs.” The frog family scientists call Ranidae are found nearly everywhere in the world, and their family includes familiar amphibians like the American Bullfrog and the European common frog. 

New research from the University of Kansas appearing in Royal Society Biology Letters shows, in contrast to expectations, “the rapid global range expansion of true frogs was not associated with increased net-diversification.”

“First, we had to identify where these true frogs came from and when they started their dispersal all over the world,” said lead author Chan Kin Onn, a doctoral student at KU’s Biodiversity Institute. “We found a distinct pattern. The origin of these frogs was Indochina — on the map today, it’s most of mainland Asia, including Thailand, Vietnam, Cambodia and Burma. True frogs dispersed throughout every continent except Antarctica from there. That’s not a new idea. But we found that a lot of this dispersal happened during a short period of time — it was during the late Eocene, about 40 million years ago. That hadn’t really been identified, until now.”

Next, Chan and co-author Rafe Brown, curator-in-charge of the KU Biodiversity Institute’s Herpetology Division, looked to see if this rapid dispersal of true frogs worldwide triggered a matching eruption of speciation. 

“That was our expectation,” Chan said. “We thought they’d take off into all this new habitat and resources, with no competition — and boom, you’d have a lot of new species. But we found the exact opposite was true. In most of the groups, nothing happened. There was no increase in speciation. In one of the groups, diversification significantly slowed down. That was the reverse of what was expected.”

To establish the actual timing of true frogs’ diversification, Chan and Brown performed phylogenetic analysis of 402 genetic samples obtained from an online database called GenBank. These samples represented 292 of the known 380 true frog species in the world.

“We mined all of these sequences and combined them into a giant analysis of the whole family,” Chain said. “It is to my knowledge the most comprehensive Ranidae phylogenetic analysis ever performed that included most of the representative species from the family.” 

Chan and Brown focused on four genes that would help to establish the family tree of true frogs.

“It’s a genealogical pedigree of specimens, a family tree of species,” Chan said.  “Normally, you think of family tree as everyone in one family and how the various people are related. But this is more expanded where we look at how species are related to each other, so you can trace ancestry back in time.”

After completing the phylogenetic analysis, the KU researchers used several frog fossils to “time calibrate” the history of the frogs’ global dispersal.

“We use fossil frogs because we can accurately date the fossils,” Chan said. “We know we found the fossil in a certain rock deposit, and we know with confidence how old the deposit is, so then we can estimate the age of the fossil.”

After Chan and Brown deduced similarities between fossilized true frogs as reported by paleontologists and contemporary true frogs, they placed fossils into groups of closely related species, which scientists call genera.

“Using data from paleontological studies, we can loosely place a fossil where in the phylogeny it belongs and can put a time stamp on that point,” Chan said. “That’s where calibration happens, each fossil is sort of like an anchor point. You can imagine with a really big phylogeny, the more anchor points or calibration points the better your time estimate.”

Through this process, the KU researchers concluded true frogs didn’t become one of the most biodiverse frog families due to dispersing into new ranges, or due to filling a gap created by a catastrophic die-off (such as the Eocene-Oligocene Extinction Event that triggered widespread extinctions from marine invertebrates to mammals in Asia and Europe).

Rather, the rich diversity of species in the Ranidae family comes from millions of years’ worth of continual evolution influenced by a host of different environs.  

“Our conclusion is kind of anticlimactic, but it’s cool because it goes against expectations,” Chan said. “We show the reason for species richness was just a really steady accumulation of species through time — there wasn’t a big event that caused this family to diversify like crazy.”

- Brendan M. Lynch, KU News

Top image: KU researchers concluded true frogs didn’t become one of the most biodiverse frog family due to dispersing into new ranges, or due to filling a gap created by a catastrophic die-off. Rather, the rich diversity of species in the Ranidae family comes from millions of years’ worth of continual evolution influenced by a host of different environs. Image by R.M. Brown.
From top right: The Rana igorota; Sangirana tipanan; Spotted stream (an Asian true frog); another Asian true frog. Photos courtesy of Chan Kin Onn, a doctoral student at KU’s Biodiversity Institute.

Herpetology